
R version 2.10.1 (2009-12-14)
Copyright (C) 2009 The R Foundation for Statistical Computing
ISBN 3-900051-07-0

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> source("/xchip/tcga/gdac_prod/applications/process_mgmt/firehose_task_registry/tcga-gdac/Correlate_Clinical_Cnvsarms_onlysig/broadinstitute.org/cancer.genome.analysis/00498/20/CNV2ClinicalAnalysis_nozzle_onlysig_arm.R")
> result <- main("/xchip/tcga/gdac_prod/applications/process_mgmt/firehose_task_registry/tcga-gdac/Correlate_Clinical_Cnvsarms_onlysig/broadinstitute.org/cancer.genome.analysis/00498/20/", "-nF=/xchip/tcga/Tools/Nozzle/v1.current", "-iD=/xchip/cga/gdac-prod/tcga-gdac/jobResults/cnvarms2cluster/STAD-TP/3143894/broad_values_by_arm.mutsig.cluster.txt", "-iC=/xchip/cga/gdac-prod/tcga-gdac/jobResults/GDAC_clinicalDataPickerPipeline/STAD-TP/3132759/1.GDAC_clinicalDataPicker.Finished/STAD-TP.clin.merged.picked.txt", "-fF=", "-fC=3", "-fH=5", "-fW=9", "-fP=OUT", "-cP=1", "-cQ=0.25", "-MF=ONLYSIG", "-oT=STAD-TP", "-nV=Nozzle.R1", "-OP=MUTSIG", "-iT=", "-iX=")
[1] "nver"          "-nV=Nozzle.R1"
[1] "nfn"                                 "/xchip/tcga/Tools/Nozzle/v1.current"
[1] "Nozzle.R1"
[1] "successfully load Nozzle.R1"
[1] "ofn"         "-oT=STAD-TP"
[1] "opt"        "-OP=MUTSIG"
[1] "tl"   "-iT="
[1] "dx"   "-iX="
[1] "opt"    "MUTSIG"
[1] "dx" ""  

nPatients in clinical file=181, in cluster file=306, common to both=180
[1] "Reduce the number of clustering variables from 80 to 74."
[1]  74 180
[1] "1p gain"
[1] 3
      1P GAIN CNV 1P GAIN WILD-TYPE 
               10               170 
      1P GAIN CNV 1P GAIN WILD-TYPE 
               10               170 
[1] "1q gain"
[1] 3
      1Q GAIN CNV 1Q GAIN WILD-TYPE 
               25               155 
      1Q GAIN CNV 1Q GAIN WILD-TYPE 
               25               155 
[1] "2p gain"
[1] 3
      2P GAIN CNV 2P GAIN WILD-TYPE 
               12               168 
      2P GAIN CNV 2P GAIN WILD-TYPE 
               12               168 
[1] "2q gain"
[1] 3
      2Q GAIN CNV 2Q GAIN WILD-TYPE 
               14               166 
      2Q GAIN CNV 2Q GAIN WILD-TYPE 
               14               166 
[1] "3p gain"
[1] 3
      3P GAIN CNV 3P GAIN WILD-TYPE 
                3               177 
      3P GAIN CNV 3P GAIN WILD-TYPE 
                3               177 
[1] "3q gain"
[1] 3
      3Q GAIN CNV 3Q GAIN WILD-TYPE 
               15               165 
      3Q GAIN CNV 3Q GAIN WILD-TYPE 
               15               165 
[1] "4p gain"
[1] 3
      4P GAIN CNV 4P GAIN WILD-TYPE 
                3               177 
      4P GAIN CNV 4P GAIN WILD-TYPE 
                3               177 
[1] "5p gain"
[1] 3
      5P GAIN CNV 5P GAIN WILD-TYPE 
               28               152 
      5P GAIN CNV 5P GAIN WILD-TYPE 
               28               152 
[1] "5q gain"
[1] 3
      5Q GAIN CNV 5Q GAIN WILD-TYPE 
                7               173 
      5Q GAIN CNV 5Q GAIN WILD-TYPE 
                7               173 
[1] "6p gain"
[1] 3
      6P GAIN CNV 6P GAIN WILD-TYPE 
               17               163 
      6P GAIN CNV 6P GAIN WILD-TYPE 
               17               163 
[1] "6q gain"
[1] 3
      6Q GAIN CNV 6Q GAIN WILD-TYPE 
               14               166 
      6Q GAIN CNV 6Q GAIN WILD-TYPE 
               14               166 
[1] "7p gain"
[1] 3
      7P GAIN CNV 7P GAIN WILD-TYPE 
               59               121 
      7P GAIN CNV 7P GAIN WILD-TYPE 
               59               121 
[1] "7q gain"
[1] 3
      7Q GAIN CNV 7Q GAIN WILD-TYPE 
               51               129 
      7Q GAIN CNV 7Q GAIN WILD-TYPE 
               51               129 
[1] "8p gain"
[1] 3
      8P GAIN CNV 8P GAIN WILD-TYPE 
               55               125 
      8P GAIN CNV 8P GAIN WILD-TYPE 
               55               125 
[1] "8q gain"
[1] 3
      8Q GAIN CNV 8Q GAIN WILD-TYPE 
               76               104 
      8Q GAIN CNV 8Q GAIN WILD-TYPE 
               76               104 
[1] "9p gain"
[1] 3
      9P GAIN CNV 9P GAIN WILD-TYPE 
               15               165 
      9P GAIN CNV 9P GAIN WILD-TYPE 
               15               165 
[1] "9q gain"
[1] 3
      9Q GAIN CNV 9Q GAIN WILD-TYPE 
               20               160 
      9Q GAIN CNV 9Q GAIN WILD-TYPE 
               20               160 
[1] "10p gain"
[1] 3
      10P GAIN CNV 10P GAIN WILD-TYPE 
                29                151 
      10P GAIN CNV 10P GAIN WILD-TYPE 
                29                151 
[1] "10q gain"
[1] 3
      10Q GAIN CNV 10Q GAIN WILD-TYPE 
                15                165 
      10Q GAIN CNV 10Q GAIN WILD-TYPE 
                15                165 
[1] "11p gain"
[1] 3
      11P GAIN CNV 11P GAIN WILD-TYPE 
                 7                173 
      11P GAIN CNV 11P GAIN WILD-TYPE 
                 7                173 
[1] "11q gain"
[1] 3
      11Q GAIN CNV 11Q GAIN WILD-TYPE 
                12                168 
      11Q GAIN CNV 11Q GAIN WILD-TYPE 
                12                168 
[1] "12p gain"
[1] 3
      12P GAIN CNV 12P GAIN WILD-TYPE 
                20                160 
      12P GAIN CNV 12P GAIN WILD-TYPE 
                20                160 
[1] "12q gain"
[1] 3
      12Q GAIN CNV 12Q GAIN WILD-TYPE 
                15                165 
      12Q GAIN CNV 12Q GAIN WILD-TYPE 
                15                165 
[1] "13q gain"
[1] 3
      13Q GAIN CNV 13Q GAIN WILD-TYPE 
                36                144 
      13Q GAIN CNV 13Q GAIN WILD-TYPE 
                36                144 
[1] "14q gain"
[1] 3
      14Q GAIN CNV 14Q GAIN WILD-TYPE 
                 3                177 
      14Q GAIN CNV 14Q GAIN WILD-TYPE 
                 3                177 
[1] "15q gain"
[1] 3
      15Q GAIN CNV 15Q GAIN WILD-TYPE 
                 8                172 
      15Q GAIN CNV 15Q GAIN WILD-TYPE 
                 8                172 
[1] "16p gain"
[1] 3
      16P GAIN CNV 16P GAIN WILD-TYPE 
                13                167 
      16P GAIN CNV 16P GAIN WILD-TYPE 
                13                167 
[1] "16q gain"
[1] 3
      16Q GAIN CNV 16Q GAIN WILD-TYPE 
                10                170 
      16Q GAIN CNV 16Q GAIN WILD-TYPE 
                10                170 
[1] "17p gain"
[1] 3
      17P GAIN CNV 17P GAIN WILD-TYPE 
                 6                174 
      17P GAIN CNV 17P GAIN WILD-TYPE 
                 6                174 
[1] "17q gain"
[1] 3
      17Q GAIN CNV 17Q GAIN WILD-TYPE 
                12                168 
      17Q GAIN CNV 17Q GAIN WILD-TYPE 
                12                168 
[1] "18p gain"
[1] 3
      18P GAIN CNV 18P GAIN WILD-TYPE 
                18                162 
      18P GAIN CNV 18P GAIN WILD-TYPE 
                18                162 
[1] "18q gain"
[1] 3
      18Q GAIN CNV 18Q GAIN WILD-TYPE 
                10                170 
      18Q GAIN CNV 18Q GAIN WILD-TYPE 
                10                170 
[1] "19p gain"
[1] 3
      19P GAIN CNV 19P GAIN WILD-TYPE 
                10                170 
      19P GAIN CNV 19P GAIN WILD-TYPE 
                10                170 
[1] "19q gain"
[1] 3
      19Q GAIN CNV 19Q GAIN WILD-TYPE 
                19                161 
      19Q GAIN CNV 19Q GAIN WILD-TYPE 
                19                161 
[1] "20p gain"
[1] 3
      20P GAIN CNV 20P GAIN WILD-TYPE 
                74                106 
      20P GAIN CNV 20P GAIN WILD-TYPE 
                74                106 
[1] "20q gain"
[1] 3
      20Q GAIN CNV 20Q GAIN WILD-TYPE 
                90                 90 
      20Q GAIN CNV 20Q GAIN WILD-TYPE 
                90                 90 
[1] "22q gain"
[1] 3
      22Q GAIN CNV 22Q GAIN WILD-TYPE 
                 3                177 
      22Q GAIN CNV 22Q GAIN WILD-TYPE 
                 3                177 
[1] "1p loss"
[1] 3
      1P LOSS CNV 1P LOSS WILD-TYPE 
               10               170 
      1P LOSS CNV 1P LOSS WILD-TYPE 
               10               170 
[1] "2p loss"
[1] 3
      2P LOSS CNV 2P LOSS WILD-TYPE 
                3               177 
      2P LOSS CNV 2P LOSS WILD-TYPE 
                3               177 
[1] "3p loss"
[1] 3
      3P LOSS CNV 3P LOSS WILD-TYPE 
               15               165 
      3P LOSS CNV 3P LOSS WILD-TYPE 
               15               165 
[1] "3q loss"
[1] 3
      3Q LOSS CNV 3Q LOSS WILD-TYPE 
                9               171 
      3Q LOSS CNV 3Q LOSS WILD-TYPE 
                9               171 
[1] "4p loss"
[1] 3
      4P LOSS CNV 4P LOSS WILD-TYPE 
               30               150 
      4P LOSS CNV 4P LOSS WILD-TYPE 
               30               150 
[1] "4q loss"
[1] 3
      4Q LOSS CNV 4Q LOSS WILD-TYPE 
               28               152 
      4Q LOSS CNV 4Q LOSS WILD-TYPE 
               28               152 
[1] "5p loss"
[1] 3
      5P LOSS CNV 5P LOSS WILD-TYPE 
               10               170 
      5P LOSS CNV 5P LOSS WILD-TYPE 
               10               170 
[1] "5q loss"
[1] 3
      5Q LOSS CNV 5Q LOSS WILD-TYPE 
               20               160 
      5Q LOSS CNV 5Q LOSS WILD-TYPE 
               20               160 
[1] "6p loss"
[1] 3
      6P LOSS CNV 6P LOSS WILD-TYPE 
                9               171 
      6P LOSS CNV 6P LOSS WILD-TYPE 
                9               171 
[1] "6q loss"
[1] 3
      6Q LOSS CNV 6Q LOSS WILD-TYPE 
               14               166 
      6Q LOSS CNV 6Q LOSS WILD-TYPE 
               14               166 
[1] "7p loss"
[1] 3
      7P LOSS CNV 7P LOSS WILD-TYPE 
                3               177 
      7P LOSS CNV 7P LOSS WILD-TYPE 
                3               177 
[1] "7q loss"
[1] 3
      7Q LOSS CNV 7Q LOSS WILD-TYPE 
                6               174 
      7Q LOSS CNV 7Q LOSS WILD-TYPE 
                6               174 
[1] "8p loss"
[1] 3
      8P LOSS CNV 8P LOSS WILD-TYPE 
               19               161 
      8P LOSS CNV 8P LOSS WILD-TYPE 
               19               161 
[1] "8q loss"
[1] 3
      8Q LOSS CNV 8Q LOSS WILD-TYPE 
                6               174 
      8Q LOSS CNV 8Q LOSS WILD-TYPE 
                6               174 
[1] "9p loss"
[1] 3
      9P LOSS CNV 9P LOSS WILD-TYPE 
               32               148 
      9P LOSS CNV 9P LOSS WILD-TYPE 
               32               148 
[1] "9q loss"
[1] 3
      9Q LOSS CNV 9Q LOSS WILD-TYPE 
               13               167 
      9Q LOSS CNV 9Q LOSS WILD-TYPE 
               13               167 
[1] "10p loss"
[1] 3
      10P LOSS CNV 10P LOSS WILD-TYPE 
                14                166 
      10P LOSS CNV 10P LOSS WILD-TYPE 
                14                166 
[1] "10q loss"
[1] 3
      10Q LOSS CNV 10Q LOSS WILD-TYPE 
                11                169 
      10Q LOSS CNV 10Q LOSS WILD-TYPE 
                11                169 
[1] "11p loss"
[1] 3
      11P LOSS CNV 11P LOSS WILD-TYPE 
                12                168 
      11P LOSS CNV 11P LOSS WILD-TYPE 
                12                168 
[1] "11q loss"
[1] 3
      11Q LOSS CNV 11Q LOSS WILD-TYPE 
                11                169 
      11Q LOSS CNV 11Q LOSS WILD-TYPE 
                11                169 
[1] "12p loss"
[1] 3
      12P LOSS CNV 12P LOSS WILD-TYPE 
                14                166 
      12P LOSS CNV 12P LOSS WILD-TYPE 
                14                166 
[1] "12q loss"
[1] 3
      12Q LOSS CNV 12Q LOSS WILD-TYPE 
                 9                171 
      12Q LOSS CNV 12Q LOSS WILD-TYPE 
                 9                171 
[1] "13q loss"
[1] 3
      13Q LOSS CNV 13Q LOSS WILD-TYPE 
                 5                175 
      13Q LOSS CNV 13Q LOSS WILD-TYPE 
                 5                175 
[1] "14q loss"
[1] 3
      14Q LOSS CNV 14Q LOSS WILD-TYPE 
                16                164 
      14Q LOSS CNV 14Q LOSS WILD-TYPE 
                16                164 
[1] "15q loss"
[1] 3
      15Q LOSS CNV 15Q LOSS WILD-TYPE 
                16                164 
      15Q LOSS CNV 15Q LOSS WILD-TYPE 
                16                164 
[1] "16p loss"
[1] 3
      16P LOSS CNV 16P LOSS WILD-TYPE 
                16                164 
      16P LOSS CNV 16P LOSS WILD-TYPE 
                16                164 
[1] "16q loss"
[1] 3
      16Q LOSS CNV 16Q LOSS WILD-TYPE 
                19                161 
      16Q LOSS CNV 16Q LOSS WILD-TYPE 
                19                161 
[1] "17p loss"
[1] 3
      17P LOSS CNV 17P LOSS WILD-TYPE 
                36                144 
      17P LOSS CNV 17P LOSS WILD-TYPE 
                36                144 
[1] "17q loss"
[1] 3
      17Q LOSS CNV 17Q LOSS WILD-TYPE 
                11                169 
      17Q LOSS CNV 17Q LOSS WILD-TYPE 
                11                169 
[1] "18p loss"
[1] 3
      18P LOSS CNV 18P LOSS WILD-TYPE 
                14                166 
      18P LOSS CNV 18P LOSS WILD-TYPE 
                14                166 
[1] "18q loss"
[1] 3
      18Q LOSS CNV 18Q LOSS WILD-TYPE 
                28                152 
      18Q LOSS CNV 18Q LOSS WILD-TYPE 
                28                152 
[1] "19p loss"
[1] 3
      19P LOSS CNV 19P LOSS WILD-TYPE 
                20                160 
      19P LOSS CNV 19P LOSS WILD-TYPE 
                20                160 
[1] "19q loss"
[1] 3
      19Q LOSS CNV 19Q LOSS WILD-TYPE 
                14                166 
      19Q LOSS CNV 19Q LOSS WILD-TYPE 
                14                166 
[1] "20p loss"
[1] 3
      20P LOSS CNV 20P LOSS WILD-TYPE 
                 5                175 
      20P LOSS CNV 20P LOSS WILD-TYPE 
                 5                175 
[1] "21q loss"
[1] 3
      21Q LOSS CNV 21Q LOSS WILD-TYPE 
                35                145 
      21Q LOSS CNV 21Q LOSS WILD-TYPE 
                35                145 
[1] "22q loss"
[1] 3
      22Q LOSS CNV 22Q LOSS WILD-TYPE 
                25                155 
      22Q LOSS CNV 22Q LOSS WILD-TYPE 
                25                155 
[1] "Xq loss"
[1] 3
      XQ LOSS CNV XQ LOSS WILD-TYPE 
                8               172 
      XQ LOSS CNV XQ LOSS WILD-TYPE 
                8               172 
[1] "data2feature, selection="
 [1] "YEARSTOBIRTH"                          
 [2] "DAYSTODEATH"                           
 [3] "DAYSTOLASTFOLLOWUP"                    
 [4] "VITALSTATUS"                           
 [5] "DCCUPLOADDATE"                         
 [6] "PRIMARYSITEOFDESEASE"                  
 [7] "GENDER"                                
 [8] "DATEOFINITIALPATHOLOGICDIAGNOSIS"      
 [9] "HISTOLOGICALTYPE"                      
[10] "PATHOLOGICSPREAD(PT)"                  
[11] "PATHOLOGICSPREAD(PN)"                  
[12] "PATHOLOGICSPREAD(M)"                   
[13] "TUMORSTAGE"                            
[14] "RADIATIONS.RADIATION.REGIMENINDICATION"
[15] "COMPLETENESS.OF.RESECTION"             
[16] "NUMBER.OF.LYMPH.NODES"                 
[17] "BATCHNUMBER"                           

Input Data has 17 rows and 180 columns.

[1] "Batch" "17"   
[1] "Last Follow UP"
TCGA-B7-5816 TCGA-B7-5818 TCGA-BR-4183 TCGA-BR-4184 TCGA-BR-4187 TCGA-BR-4188 
         171            3           NA           NA           NA           NA 
TCGA-BR-4191 TCGA-BR-4201 TCGA-BR-4253 TCGA-BR-4255 TCGA-BR-4256 TCGA-BR-4257 
          NA           NA           NA           NA           NA           NA 
TCGA-BR-4267 TCGA-BR-4279 TCGA-BR-4280 TCGA-BR-4292 TCGA-BR-4294 TCGA-BR-4357 
          NA           NA           NA           NA           NA           NA 
TCGA-BR-4361 TCGA-BR-4362 TCGA-BR-4363 TCGA-BR-4366 TCGA-BR-4367 TCGA-BR-4368 
          NA           NA           NA           NA           NA           NA 
TCGA-BR-4369 TCGA-BR-4370 TCGA-BR-4371 TCGA-BR-6452 TCGA-BR-6453 TCGA-BR-6454 
          NA           NA           NA           29           NA           NA 
TCGA-BR-6455 TCGA-BR-6456 TCGA-BR-6457 TCGA-BR-6458 TCGA-BR-6563 TCGA-BR-6564 
          43           NA           41           41           26           25 
TCGA-BR-6565 TCGA-BR-6566 TCGA-BR-6705 TCGA-BR-6706 TCGA-BR-6707 TCGA-BR-6709 
          19           19           52           66           30           37 
TCGA-BR-6710 TCGA-BR-6801 TCGA-BR-6802 TCGA-BR-6803 TCGA-BR-6852 TCGA-BR-7196 
          20           34           23           20            8           37 
TCGA-BR-7197 TCGA-BR-7703 TCGA-BR-7704 TCGA-BR-7707 TCGA-BR-7715 TCGA-BR-7716 
          45           14           38            4           32           25 
TCGA-BR-7717 TCGA-BR-7722 TCGA-BR-7723 TCGA-BR-7851 TCGA-BR-7901 TCGA-BR-7957 
          21            5          138           30           29           21 
TCGA-BR-7958 TCGA-BR-7959 TCGA-BR-8059 TCGA-BR-8060 TCGA-BR-8077 TCGA-BR-8078 
           5           33           25           40           21           29 
TCGA-BR-8080 TCGA-BR-8081 TCGA-BR-8284 TCGA-BR-8285 TCGA-BR-8286 TCGA-BR-8289 
          15           14           22            8           13            8 
TCGA-BR-8291 TCGA-BR-8295 TCGA-BR-8296 TCGA-BR-8297 TCGA-BR-8592 TCGA-BR-A4IU 
          36           47           45           23            6           18 
TCGA-BR-A4IV TCGA-BR-A4IY TCGA-BR-A4IZ TCGA-BR-A4J1 TCGA-BR-A4J2 TCGA-BR-A4J4 
          28           12           24           NA           24           16 
TCGA-BR-A4J5 TCGA-BR-A4J6 TCGA-BR-A4J8 TCGA-BR-A4J9 TCGA-BR-A4PF TCGA-BR-A4QI 
          13            4            7            3           22           15 
TCGA-BR-A4QL TCGA-CD-5798 TCGA-CD-5799 TCGA-CD-5800 TCGA-CD-5801 TCGA-CD-5802 
          68           25           21           11           15            9 
TCGA-CD-5803 TCGA-CD-5804 TCGA-CG-4300 TCGA-CG-4301 TCGA-CG-4304 TCGA-CG-4305 
           2           NA          609           92          822          485 
TCGA-CG-4306 TCGA-CG-4436 TCGA-CG-4437 TCGA-CG-4438 TCGA-CG-4440 TCGA-CG-4441 
          31         1611          245         1644          122          426 
TCGA-CG-4442 TCGA-CG-4443 TCGA-CG-4444 TCGA-CG-4449 TCGA-CG-4455 TCGA-CG-4460 
          NA          912         1431          580          366          669 
TCGA-CG-4462 TCGA-CG-4465 TCGA-CG-4466 TCGA-CG-4469 TCGA-CG-4472 TCGA-CG-4474 
          31          273          576          215          365           31 
TCGA-CG-4475 TCGA-CG-4476 TCGA-CG-4477 TCGA-CG-5716 TCGA-CG-5717 TCGA-CG-5718 
          NA           NA           31           31          211           31 
TCGA-CG-5719 TCGA-CG-5720 TCGA-CG-5721 TCGA-CG-5722 TCGA-CG-5723 TCGA-CG-5724 
          31           30          182           29         2131          366 
TCGA-CG-5725 TCGA-CG-5726 TCGA-CG-5727 TCGA-CG-5728 TCGA-CG-5730 TCGA-CG-5732 
         457          881          944         1980          122         1674 
TCGA-CG-5733 TCGA-CG-5734 TCGA-D7-5577 TCGA-D7-5578 TCGA-D7-5579 TCGA-D7-6518 
         641          243          263          109          138          298 
TCGA-D7-6519 TCGA-D7-6520 TCGA-D7-6521 TCGA-D7-6522 TCGA-D7-6524 TCGA-D7-6525 
         476          293          249          210           21          181 
TCGA-D7-6526 TCGA-D7-6527 TCGA-D7-6528 TCGA-D7-6815 TCGA-D7-6817 TCGA-D7-6818 
         201          126           51          111          143          123 
TCGA-D7-6820 TCGA-D7-6822 TCGA-EQ-5647 TCGA-EQ-8122 TCGA-F1-6177 TCGA-F1-6874 
          89          130           19          237          199           61 
TCGA-F1-6875 TCGA-FP-7735 TCGA-FP-7829 TCGA-FP-7916 TCGA-FP-7998 TCGA-FP-8099 
          NA           12            6           92          109           31 
TCGA-FP-8209 TCGA-FP-8210 TCGA-FP-8631 TCGA-HF-7131 TCGA-HF-7132 TCGA-HF-7133 
          NA           NA           17           NA           NA           NA 
TCGA-HF-7134 TCGA-HF-7136 TCGA-HJ-7597 TCGA-IN-7806 TCGA-IN-7808 TCGA-IP-7968 
          NA           NA           NA          209          108           77 
Variable 1:'AGE':	nDistinctValues=48,	numeric=TRUE,	binary=FALSE,	exclude=FALSE.
Variable 2:'DAYSTODEATH':	nDistinctValues=19,	numeric=TRUE,	binary=FALSE,	exclude=TRUE.
Variable 3:'DAYSTOLASTFOLLOWUP':	nDistinctValues=95,	numeric=TRUE,	binary=FALSE,	exclude=TRUE.
Variable 4:'VITALSTATUS':	nDistinctValues=2,	numeric=TRUE,	binary=TRUE,	exclude=FALSE.
Variable 5:'DCCUPLOADDAY':	nDistinctValues=5,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
Variable 6:'PRIMARY.SITE.OF.DISEASE':	nDistinctValues=1,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
Variable 7:'GENDER':	nDistinctValues=2,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 8:'DAYOFINITIALPATHOLOGICDIAGNOSIS':	nDistinctValues=11,	numeric=TRUE,	binary=FALSE,	exclude=TRUE.
Variable 9:'HISTOLOGICAL.TYPE':	nDistinctValues=11,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 10:'PATHOLOGY.T':	nDistinctValues=11,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 11:'PATHOLOGY.N':	nDistinctValues=6,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 12:'PATHOLOGICSPREAD(M)':	nDistinctValues=3,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 13:'TUMOR.STAGE':	nDistinctValues=11,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 14:'RADIATIONS.RADIATION.REGIMENINDICATION':	nDistinctValues=2,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 15:'COMPLETENESS.OF.RESECTION':	nDistinctValues=4,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 16:'NUMBER.OF.LYMPH.NODES':	nDistinctValues=27,	numeric=TRUE,	binary=FALSE,	exclude=FALSE.
Variable 17:'BATCH.NUMBER':	nDistinctValues=11,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
[1] "rownames(nsurv.mat)"
 [1] "AGE"                                   
 [2] "GENDER"                                
 [3] "HISTOLOGICAL.TYPE"                     
 [4] "PATHOLOGY.T"                           
 [5] "PATHOLOGY.N"                           
 [6] "PATHOLOGICSPREAD(M)"                   
 [7] "TUMOR.STAGE"                           
 [8] "RADIATIONS.RADIATION.REGIMENINDICATION"
 [9] "COMPLETENESS.OF.RESECTION"             
[10] "NUMBER.OF.LYMPH.NODES"                 
[1] "TUMOR.?STAGE" "7"           
[1] "stage2"
vv
 1  2  3  4 
24 37 39 26 
[1] "TUMOR.?GRADE"
[1] "PATHOLOGY.T" "4"          
[1] "PATHOLOGY.N" "5"          
Output Data has 180 columns, 1 survival variables, and 10 non-survival variables.
AGE, nv=48, binary=FALSE, numeric=TRUE
GENDER, nv=2, binary=FALSE, numeric=FALSE
HISTOLOGICAL.TYPE, nv=11, binary=FALSE, numeric=FALSE
PATHOLOGY.T, nv=4, binary=FALSE, numeric=TRUE
[1] "grepl('PATHOLOGY.T',vnm)"
vv
T1 T2 T3 T4 
 6 52 56 18 
[1] "table(vv)"
vv
T1 T2 T3 T4 
 6 52 56 18 
$ClinVariableName
[1] "PATHOLOGY.T"

$Table
vv
T1 T2 T3 T4 
 6 52 56 18 

$nClasses
[1] 4

$ClinVariableType
[1] "multiclass(4)"


T1 T2 T3 T4 
 6 52 56 18 
PATHOLOGY.N, nv=4, binary=FALSE, numeric=TRUE
[1] "grepl('PATHOLOGY.N',vnm)"
vv
N0 N1 N2 N3 
44 49 23 15 
[1] "table(vv)"
vv
N0 N1 N2 N3 
44 49 23 15 
$ClinVariableName
[1] "PATHOLOGY.N"

$Table
vv
N0 N1 N2 N3 
44 49 23 15 

$nClasses
[1] 4

$ClinVariableType
[1] "multiclass(4)"


N0 N1 N2 N3 
44 49 23 15 
PATHOLOGICSPREAD(M), nv=3, binary=FALSE, numeric=FALSE
TUMOR.STAGE, nv=4, binary=FALSE, numeric=TRUE
[1] "grepl('TUMOR.?STAGE$',vnm)"
vv
  I  II III  IV 
 24  37  39  26 
[1] "table(vv)"
vv
  I  II III  IV 
 24  37  39  26 
$ClinVariableName
[1] "TUMOR.STAGE"

$Table
vv
  I  II III  IV 
 24  37  39  26 

$nClasses
[1] 4

$ClinVariableType
[1] "multiclass(4)"


  I  II III  IV 
 24  37  39  26 
RADIATIONS.RADIATION.REGIMENINDICATION, nv=2, binary=FALSE, numeric=FALSE
COMPLETENESS.OF.RESECTION, nv=4, binary=FALSE, numeric=FALSE
NUMBER.OF.LYMPH.NODES, nv=27, binary=FALSE, numeric=TRUE

Clustering(1) Variable = 1p gain
D1V1, survival
                   sevent
clus2                 0   1
  1P GAIN CNV         5   0
  1P GAIN WILD-TYPE 119  19
      1P GAIN CNV 1P GAIN WILD-TYPE 
                5               138 
      1P GAIN CNV 1P GAIN WILD-TYPE 
                0                19 
$`1P GAIN CNV`
TCGA-BR-7717 TCGA-BR-8286 TCGA-BR-A4J8 TCGA-EQ-8122 TCGA-IN-7808 
        0.69         0.43         0.23         7.79         3.55 

$`1P GAIN WILD-TYPE`
TCGA-B7-5816 TCGA-B7-5818 TCGA-BR-6452 TCGA-BR-6455 TCGA-BR-6457 TCGA-BR-6458 
        5.62         0.10         0.95         1.41         1.35         1.35 
TCGA-BR-6563 TCGA-BR-6564 TCGA-BR-6565 TCGA-BR-6566 TCGA-BR-6705 TCGA-BR-6706 
        0.85         0.82         0.62         0.62         1.71         2.17 
TCGA-BR-6707 TCGA-BR-6709 TCGA-BR-6710 TCGA-BR-6801 TCGA-BR-6802 TCGA-BR-6803 
        0.99         1.22         0.66         1.12         0.76         0.66 
TCGA-BR-6852 TCGA-BR-7196 TCGA-BR-7197 TCGA-BR-7703 TCGA-BR-7704 TCGA-BR-7707 
        0.26         1.22         1.48         0.46         1.25         0.13 
TCGA-BR-7715 TCGA-BR-7716 TCGA-BR-7722 TCGA-BR-7723 TCGA-BR-7851 TCGA-BR-7901 
        1.05         0.82         0.16         4.54         0.99         0.95 
TCGA-BR-7957 TCGA-BR-7958 TCGA-BR-7959 TCGA-BR-8059 TCGA-BR-8060 TCGA-BR-8077 
        0.69         0.16         1.08         0.82         1.32         0.69 
TCGA-BR-8078 TCGA-BR-8080 TCGA-BR-8081 TCGA-BR-8284 TCGA-BR-8285 TCGA-BR-8289 
        0.95         0.49         0.46         0.72         0.26         0.26 
TCGA-BR-8291 TCGA-BR-8295 TCGA-BR-8296 TCGA-BR-8297 TCGA-BR-8592 TCGA-BR-A4IU 
        1.18         1.55         1.48         0.76         0.20         0.59 
TCGA-BR-A4IV TCGA-BR-A4IY TCGA-BR-A4IZ TCGA-BR-A4J1 TCGA-BR-A4J2 TCGA-BR-A4J4 
        0.92         0.39         0.79         0.72         0.79         0.53 
TCGA-BR-A4J5 TCGA-BR-A4J6 TCGA-BR-A4J9 TCGA-BR-A4PF TCGA-BR-A4QI TCGA-BR-A4QL 
        0.43         0.13         0.10         0.72         0.49         2.24 
TCGA-CD-5798 TCGA-CD-5799 TCGA-CD-5800 TCGA-CD-5801 TCGA-CD-5802 TCGA-CD-5803 
        0.82         0.69         0.36         0.49         0.30         0.07 
TCGA-CG-4300 TCGA-CG-4301 TCGA-CG-4304 TCGA-CG-4305 TCGA-CG-4306 TCGA-CG-4436 
       20.02         3.02        27.02        15.95         1.02        52.96 
TCGA-CG-4437 TCGA-CG-4438 TCGA-CG-4440 TCGA-CG-4441 TCGA-CG-4443 TCGA-CG-4444 
        8.05        54.05         4.01        14.01        29.98        47.05 
TCGA-CG-4449 TCGA-CG-4455 TCGA-CG-4460 TCGA-CG-4462 TCGA-CG-4465 TCGA-CG-4466 
       19.07        12.03        21.99         1.02         8.98        18.94 
TCGA-CG-4469 TCGA-CG-4472 TCGA-CG-4474 TCGA-CG-4477 TCGA-CG-5716 TCGA-CG-5717 
        7.07        12.00         1.02         1.02         1.02         6.94 
TCGA-CG-5718 TCGA-CG-5719 TCGA-CG-5720 TCGA-CG-5721 TCGA-CG-5722 TCGA-CG-5723 
        1.02         1.02         0.99         5.98         0.95        70.06 
TCGA-CG-5724 TCGA-CG-5725 TCGA-CG-5726 TCGA-CG-5727 TCGA-CG-5728 TCGA-CG-5730 
       12.03        15.02        28.96        31.04        65.10         4.01 
TCGA-CG-5732 TCGA-CG-5733 TCGA-CG-5734 TCGA-D7-5577 TCGA-D7-5578 TCGA-D7-5579 
       55.04        21.07         7.99         8.65         3.58         4.54 
TCGA-D7-6518 TCGA-D7-6519 TCGA-D7-6520 TCGA-D7-6521 TCGA-D7-6522 TCGA-D7-6524 
        9.80        15.65         9.63         8.19         6.90         0.69 
TCGA-D7-6525 TCGA-D7-6526 TCGA-D7-6527 TCGA-D7-6528 TCGA-D7-6815 TCGA-D7-6817 
        5.95         6.61         4.14         1.68         3.65         4.70 
TCGA-D7-6818 TCGA-D7-6820 TCGA-D7-6822 TCGA-EQ-5647 TCGA-F1-6177 TCGA-F1-6874 
        4.04         2.93         4.27         0.62         6.54         2.01 
TCGA-F1-6875 TCGA-FP-7735 TCGA-FP-7829 TCGA-FP-7916 TCGA-FP-7998 TCGA-FP-8099 
       72.23         0.39         0.20         3.02         3.58         1.02 
TCGA-FP-8209 TCGA-FP-8210 TCGA-FP-8631 TCGA-HJ-7597 TCGA-IN-7806 TCGA-IP-7968 
       59.05         5.03         0.56        26.43         6.87         2.53 

      1P GAIN CNV 1P GAIN WILD-TYPE 
             0.23              0.07 
      1P GAIN CNV 1P GAIN WILD-TYPE 
             7.79             72.23 
      1P GAIN CNV 1P GAIN WILD-TYPE 
            0.690             1.285 
[1] "0.2 - 7.8 (0.7)"  "0.1 - 72.2 (1.3)"
       TCGA-B7-5816        TCGA-B7-5818        TCGA-BR-6452        TCGA-BR-6455 
"1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" 
       TCGA-BR-6457        TCGA-BR-6458        TCGA-BR-6563        TCGA-BR-6564 
"1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" 
       TCGA-BR-6565        TCGA-BR-6566        TCGA-BR-6705        TCGA-BR-6706 
"1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" 
       TCGA-BR-6707        TCGA-BR-6709        TCGA-BR-6710        TCGA-BR-6801 
"1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" 
       TCGA-BR-6802        TCGA-BR-6803        TCGA-BR-6852        TCGA-BR-7196 
"1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" 
       TCGA-BR-7197        TCGA-BR-7703        TCGA-BR-7704        TCGA-BR-7707 
"1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" 
       TCGA-BR-7715        TCGA-BR-7716        TCGA-BR-7717        TCGA-BR-7722 
"1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE"       "1P GAIN CNV" "1P GAIN WILD-TYPE" 
       TCGA-BR-7723        TCGA-BR-7851        TCGA-BR-7901        TCGA-BR-7957 
"1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" 
       TCGA-BR-7958        TCGA-BR-7959        TCGA-BR-8059        TCGA-BR-8060 
"1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" 
       TCGA-BR-8077        TCGA-BR-8078        TCGA-BR-8080        TCGA-BR-8081 
"1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" 
       TCGA-BR-8284        TCGA-BR-8285        TCGA-BR-8286        TCGA-BR-8289 
"1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE"       "1P GAIN CNV" "1P GAIN WILD-TYPE" 
       TCGA-BR-8291        TCGA-BR-8295        TCGA-BR-8296        TCGA-BR-8297 
"1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" 
       TCGA-BR-8592        TCGA-BR-A4IU        TCGA-BR-A4IV        TCGA-BR-A4IY 
"1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" 
       TCGA-BR-A4IZ        TCGA-BR-A4J1        TCGA-BR-A4J2        TCGA-BR-A4J4 
"1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" 
       TCGA-BR-A4J5        TCGA-BR-A4J6        TCGA-BR-A4J8        TCGA-BR-A4J9 
"1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE"       "1P GAIN CNV" "1P GAIN WILD-TYPE" 
       TCGA-BR-A4PF        TCGA-BR-A4QI        TCGA-BR-A4QL        TCGA-CD-5798 
"1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" 
       TCGA-CD-5799        TCGA-CD-5800        TCGA-CD-5801        TCGA-CD-5802 
"1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" 
       TCGA-CD-5803        TCGA-CG-4300        TCGA-CG-4301        TCGA-CG-4304 
"1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" 
       TCGA-CG-4305        TCGA-CG-4306        TCGA-CG-4436        TCGA-CG-4437 
"1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" 
       TCGA-CG-4438        TCGA-CG-4440        TCGA-CG-4441        TCGA-CG-4443 
"1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" 
       TCGA-CG-4444        TCGA-CG-4449        TCGA-CG-4455        TCGA-CG-4460 
"1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" 
       TCGA-CG-4462        TCGA-CG-4465        TCGA-CG-4466        TCGA-CG-4469 
"1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" 
       TCGA-CG-4472        TCGA-CG-4474        TCGA-CG-4477        TCGA-CG-5716 
"1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" 
       TCGA-CG-5717        TCGA-CG-5718        TCGA-CG-5719        TCGA-CG-5720 
"1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" 
       TCGA-CG-5721        TCGA-CG-5722        TCGA-CG-5723        TCGA-CG-5724 
"1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" 
       TCGA-CG-5725        TCGA-CG-5726        TCGA-CG-5727        TCGA-CG-5728 
"1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" 
       TCGA-CG-5730        TCGA-CG-5732        TCGA-CG-5733        TCGA-CG-5734 
"1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" 
       TCGA-D7-5577        TCGA-D7-5578        TCGA-D7-5579        TCGA-D7-6518 
"1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" 
       TCGA-D7-6519        TCGA-D7-6520        TCGA-D7-6521        TCGA-D7-6522 
"1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" 
       TCGA-D7-6524        TCGA-D7-6525        TCGA-D7-6526        TCGA-D7-6527 
"1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" 
       TCGA-D7-6528        TCGA-D7-6815        TCGA-D7-6817        TCGA-D7-6818 
"1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" 
       TCGA-D7-6820        TCGA-D7-6822        TCGA-EQ-5647        TCGA-EQ-8122 
"1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE"       "1P GAIN CNV" 
       TCGA-F1-6177        TCGA-F1-6874        TCGA-F1-6875        TCGA-FP-7735 
"1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" 
       TCGA-FP-7829        TCGA-FP-7916        TCGA-FP-7998        TCGA-FP-8099 
"1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" 
       TCGA-FP-8209        TCGA-FP-8210        TCGA-FP-8631        TCGA-HJ-7597 
"1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" 
       TCGA-IN-7806        TCGA-IN-7808        TCGA-IP-7968 
"1P GAIN WILD-TYPE"       "1P GAIN CNV" "1P GAIN WILD-TYPE" 
       TCGA-B7-5816        TCGA-B7-5818        TCGA-BR-6452        TCGA-BR-6455 
"1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" 
       TCGA-BR-6457        TCGA-BR-6458        TCGA-BR-6563        TCGA-BR-6564 
"1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" 
       TCGA-BR-6565        TCGA-BR-6566        TCGA-BR-6705        TCGA-BR-6706 
"1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" 
       TCGA-BR-6707        TCGA-BR-6709        TCGA-BR-6710        TCGA-BR-6801 
"1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" 
       TCGA-BR-6802        TCGA-BR-6803        TCGA-BR-6852        TCGA-BR-7196 
"1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" 
       TCGA-BR-7197        TCGA-BR-7703        TCGA-BR-7704        TCGA-BR-7707 
"1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" 
       TCGA-BR-7715        TCGA-BR-7716        TCGA-BR-7717        TCGA-BR-7722 
"1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE"       "1P GAIN CNV" "1P GAIN WILD-TYPE" 
       TCGA-BR-7723        TCGA-BR-7851        TCGA-BR-7901        TCGA-BR-7957 
"1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" 
       TCGA-BR-7958        TCGA-BR-7959        TCGA-BR-8059        TCGA-BR-8060 
"1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" 
       TCGA-BR-8077        TCGA-BR-8078        TCGA-BR-8080        TCGA-BR-8081 
"1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" 
       TCGA-BR-8284        TCGA-BR-8285        TCGA-BR-8286        TCGA-BR-8289 
"1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE"       "1P GAIN CNV" "1P GAIN WILD-TYPE" 
       TCGA-BR-8291        TCGA-BR-8295        TCGA-BR-8296        TCGA-BR-8297 
"1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" 
       TCGA-BR-8592        TCGA-BR-A4IU        TCGA-BR-A4IV        TCGA-BR-A4IY 
"1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" 
       TCGA-BR-A4IZ        TCGA-BR-A4J1        TCGA-BR-A4J2        TCGA-BR-A4J4 
"1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" 
       TCGA-BR-A4J5        TCGA-BR-A4J6        TCGA-BR-A4J8        TCGA-BR-A4J9 
"1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE"       "1P GAIN CNV" "1P GAIN WILD-TYPE" 
       TCGA-BR-A4PF        TCGA-BR-A4QI        TCGA-BR-A4QL        TCGA-CD-5798 
"1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" 
       TCGA-CD-5799        TCGA-CD-5800        TCGA-CD-5801        TCGA-CD-5802 
"1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" 
       TCGA-CD-5803        TCGA-CG-4300        TCGA-CG-4301        TCGA-CG-4304 
"1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" 
       TCGA-CG-4305        TCGA-CG-4306        TCGA-CG-4436        TCGA-CG-4437 
"1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" 
       TCGA-CG-4438        TCGA-CG-4440        TCGA-CG-4441        TCGA-CG-4443 
"1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" 
       TCGA-CG-4444        TCGA-CG-4449        TCGA-CG-4455        TCGA-CG-4460 
"1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" 
       TCGA-CG-4462        TCGA-CG-4465        TCGA-CG-4466        TCGA-CG-4469 
"1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" 
       TCGA-CG-4472        TCGA-CG-4474        TCGA-CG-4477        TCGA-CG-5716 
"1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" 
       TCGA-CG-5717        TCGA-CG-5718        TCGA-CG-5719        TCGA-CG-5720 
"1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" 
       TCGA-CG-5721        TCGA-CG-5722        TCGA-CG-5723        TCGA-CG-5724 
"1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" 
       TCGA-CG-5725        TCGA-CG-5726        TCGA-CG-5727        TCGA-CG-5728 
"1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" 
       TCGA-CG-5730        TCGA-CG-5732        TCGA-CG-5733        TCGA-CG-5734 
"1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" 
       TCGA-D7-5577        TCGA-D7-5578        TCGA-D7-5579        TCGA-D7-6518 
"1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" 
       TCGA-D7-6519        TCGA-D7-6520        TCGA-D7-6521        TCGA-D7-6522 
"1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" 
       TCGA-D7-6524        TCGA-D7-6525        TCGA-D7-6526        TCGA-D7-6527 
"1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" 
       TCGA-D7-6528        TCGA-D7-6815        TCGA-D7-6817        TCGA-D7-6818 
"1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" 
       TCGA-D7-6820        TCGA-D7-6822        TCGA-EQ-5647        TCGA-EQ-8122 
"1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE"       "1P GAIN CNV" 
       TCGA-F1-6177        TCGA-F1-6874        TCGA-F1-6875        TCGA-FP-7735 
"1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" 
       TCGA-FP-7829        TCGA-FP-7916        TCGA-FP-7998        TCGA-FP-8099 
"1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" 
       TCGA-FP-8209        TCGA-FP-8210        TCGA-FP-8631        TCGA-HJ-7597 
"1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" 
       TCGA-IN-7806        TCGA-IN-7808        TCGA-IP-7968 
"1P GAIN WILD-TYPE"       "1P GAIN CNV" "1P GAIN WILD-TYPE" 
       TCGA-B7-5816        TCGA-B7-5818        TCGA-BR-6452        TCGA-BR-6455 
"1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" 
       TCGA-BR-6457        TCGA-BR-6458        TCGA-BR-6563        TCGA-BR-6564 
"1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" 
       TCGA-BR-6565        TCGA-BR-6566        TCGA-BR-6705        TCGA-BR-6706 
"1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" 
       TCGA-BR-6707        TCGA-BR-6709        TCGA-BR-6710        TCGA-BR-6801 
"1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" 
       TCGA-BR-6802        TCGA-BR-6803        TCGA-BR-6852        TCGA-BR-7196 
"1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" 
       TCGA-BR-7197        TCGA-BR-7703        TCGA-BR-7704        TCGA-BR-7707 
"1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" 
       TCGA-BR-7715        TCGA-BR-7716        TCGA-BR-7717        TCGA-BR-7722 
"1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE"       "1P GAIN CNV" "1P GAIN WILD-TYPE" 
       TCGA-BR-7723        TCGA-BR-7851        TCGA-BR-7901        TCGA-BR-7957 
"1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" 
       TCGA-BR-7958        TCGA-BR-7959        TCGA-BR-8059        TCGA-BR-8060 
"1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" 
       TCGA-BR-8077        TCGA-BR-8078        TCGA-BR-8080        TCGA-BR-8081 
"1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" 
       TCGA-BR-8284        TCGA-BR-8285        TCGA-BR-8286        TCGA-BR-8289 
"1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE"       "1P GAIN CNV" "1P GAIN WILD-TYPE" 
       TCGA-BR-8291        TCGA-BR-8295        TCGA-BR-8296        TCGA-BR-8297 
"1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" 
       TCGA-BR-8592        TCGA-BR-A4IU        TCGA-BR-A4IV        TCGA-BR-A4IY 
"1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" 
       TCGA-BR-A4IZ        TCGA-BR-A4J1        TCGA-BR-A4J2        TCGA-BR-A4J4 
"1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" 
       TCGA-BR-A4J5        TCGA-BR-A4J6        TCGA-BR-A4J8        TCGA-BR-A4J9 
"1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE"       "1P GAIN CNV" "1P GAIN WILD-TYPE" 
       TCGA-BR-A4PF        TCGA-BR-A4QI        TCGA-BR-A4QL        TCGA-CD-5798 
"1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" 
       TCGA-CD-5799        TCGA-CD-5800        TCGA-CD-5801        TCGA-CD-5802 
"1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" 
       TCGA-CD-5803        TCGA-CG-4300        TCGA-CG-4301        TCGA-CG-4304 
"1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" 
       TCGA-CG-4305        TCGA-CG-4306        TCGA-CG-4436        TCGA-CG-4437 
"1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" 
       TCGA-CG-4438        TCGA-CG-4440        TCGA-CG-4441        TCGA-CG-4443 
"1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" 
       TCGA-CG-4444        TCGA-CG-4449        TCGA-CG-4455        TCGA-CG-4460 
"1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" 
       TCGA-CG-4462        TCGA-CG-4465        TCGA-CG-4466        TCGA-CG-4469 
"1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" 
       TCGA-CG-4472        TCGA-CG-4474        TCGA-CG-4477        TCGA-CG-5716 
"1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" 
       TCGA-CG-5717        TCGA-CG-5718        TCGA-CG-5719        TCGA-CG-5720 
"1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" 
       TCGA-CG-5721        TCGA-CG-5722        TCGA-CG-5723        TCGA-CG-5724 
"1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" 
       TCGA-CG-5725        TCGA-CG-5726        TCGA-CG-5727        TCGA-CG-5728 
"1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" 
       TCGA-CG-5730        TCGA-CG-5732        TCGA-CG-5733        TCGA-CG-5734 
"1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" 
       TCGA-D7-5577        TCGA-D7-5578        TCGA-D7-5579        TCGA-D7-6518 
"1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" 
       TCGA-D7-6519        TCGA-D7-6520        TCGA-D7-6521        TCGA-D7-6522 
"1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" 
       TCGA-D7-6524        TCGA-D7-6525        TCGA-D7-6526        TCGA-D7-6527 
"1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" 
       TCGA-D7-6528        TCGA-D7-6815        TCGA-D7-6817        TCGA-D7-6818 
"1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" 
       TCGA-D7-6820        TCGA-D7-6822        TCGA-EQ-5647        TCGA-EQ-8122 
"1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE"       "1P GAIN CNV" 
       TCGA-F1-6177        TCGA-F1-6874        TCGA-F1-6875        TCGA-FP-7735 
"1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" 
       TCGA-FP-7829        TCGA-FP-7916        TCGA-FP-7998        TCGA-FP-8099 
"1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" 
       TCGA-FP-8209        TCGA-FP-8210        TCGA-FP-8631        TCGA-HJ-7597 
"1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" 
       TCGA-IN-7806        TCGA-IN-7808        TCGA-IP-7968 
"1P GAIN WILD-TYPE"       "1P GAIN CNV" "1P GAIN WILD-TYPE" 
[1] "hr="     "9200000"
D1V2, continuous
D1V3, binary
[1] "tbl2"
                   cls
clus                [,1] [,2]
  1P GAIN CNV          3    7
  1P GAIN WILD-TYPE   69  101
        clus
vv       1P GAIN CNV 1P GAIN WILD-TYPE
  FEMALE           3                69
  MALE             7               101
                   vv
clus                STOMACH  ADENOCARCINOMA  DIFFUSE TYPE
  1P GAIN CNV                                           0
  1P GAIN WILD-TYPE                                    10
                   vv
clus                STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  1P GAIN CNV                                                            2
  1P GAIN WILD-TYPE                                                     14
                   vv
clus                STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  1P GAIN CNV                                                                       1
  1P GAIN WILD-TYPE                                                                 7
                   vv
clus                STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE
  1P GAIN CNV                                                              0
  1P GAIN WILD-TYPE                                                        3
                   vv
clus                STOMACH ADENOCARCINOMA  SIGNET RING TYPE
  1P GAIN CNV                                              0
  1P GAIN WILD-TYPE                                        1
                   vv
clus                STOMACH ADENOCARCINOMA - DIFFUSE TYPE
  1P GAIN CNV                                           1
  1P GAIN WILD-TYPE                                    15
                   vv
clus                STOMACH ADENOCARCINOMA - NOT OTHERWISE SPECIFIED (NOS)
  1P GAIN CNV                                                            6
  1P GAIN WILD-TYPE                                                     67
                   vv
clus                STOMACH INTESTINAL ADENOCARCINOMA - MUCINOUS TYPE
  1P GAIN CNV                                                       0
  1P GAIN WILD-TYPE                                                 7
                   vv
clus                STOMACH INTESTINAL ADENOCARCINOMA - PAPILLARY TYPE
  1P GAIN CNV                                                        0
  1P GAIN WILD-TYPE                                                  3
                   vv
clus                STOMACH INTESTINAL ADENOCARCINOMA - TUBULAR TYPE
  1P GAIN CNV                                                      0
  1P GAIN WILD-TYPE                                               10
                   vv
clus                STOMACH INTESTINAL ADENOCARCINOMA - TYPE NOT OTHERWISE SPECIFIED (NOS)
  1P GAIN CNV                                                                            0
  1P GAIN WILD-TYPE                                                                     28
D1V4, multiclass
                   vv
clus                T1 T2 T3 T4
  1P GAIN CNV        0  1  3  1
  1P GAIN WILD-TYPE  6 51 53 17
D1V5, multiclass
    clus
vv   1P GAIN CNV 1P GAIN WILD-TYPE
  T1           0                 6
  T2           1                51
  T3           3                53
  T4           1                17
                   vv
clus                N0 N1 N2 N3
  1P GAIN CNV        1  2  0  1
  1P GAIN WILD-TYPE 43 47 23 14
D1V6, multiclass
    clus
vv   1P GAIN CNV 1P GAIN WILD-TYPE
  N0           1                43
  N1           2                47
  N2           0                23
  N3           1                14
                   vv
clus                 M0  M1  MX
  1P GAIN CNV         5   1   1
  1P GAIN WILD-TYPE 113  15   7
D1V7, multiclass
    clus
vv   1P GAIN CNV 1P GAIN WILD-TYPE
  M0           5               113
  M1           1                15
  MX           1                 7
                   vv
clus                 I II III IV
  1P GAIN CNV        1  0   2  1
  1P GAIN WILD-TYPE 23 37  37 25
D1V8, multiclass
     clus
vv    1P GAIN CNV 1P GAIN WILD-TYPE
  I             1                23
  II            0                37
  III           2                37
  IV            1                25
D1V9, binary
[1] "tbl2"
                   cls
clus                [,1] [,2]
  1P GAIN CNV          0   10
  1P GAIN WILD-TYPE    5  165
     clus
vv    1P GAIN CNV 1P GAIN WILD-TYPE
  NO            0                 5
  YES          10               165
                   vv
clus                 R0  R1  R2  RX
  1P GAIN CNV         4   0   0   4
  1P GAIN WILD-TYPE 121   7  12  21
D1V10, multiclass
    clus
vv   1P GAIN CNV 1P GAIN WILD-TYPE
  R0           4               121
  R1           0                 7
  R2           0                12
  RX           4                21
D1V11, continuous

Clustering(2) Variable = 1q gain
D2V1, survival
                   sevent
clus2                 0   1
  1Q GAIN CNV        14   3
  1Q GAIN WILD-TYPE 110  16
      1Q GAIN CNV 1Q GAIN WILD-TYPE 
               17               126 
      1Q GAIN CNV 1Q GAIN WILD-TYPE 
                3                16 
$`1Q GAIN CNV`
TCGA-BR-7717 TCGA-BR-7723 TCGA-BR-8286 TCGA-BR-8295 TCGA-BR-A4J8 TCGA-CG-4460 
        0.69         4.54         0.43         1.55         0.23        21.99 
TCGA-D7-6526 TCGA-D7-6527 TCGA-D7-6817 TCGA-D7-6818 TCGA-D7-6822 TCGA-EQ-5647 
        6.61         4.14         4.70         4.04         4.27         0.62 
TCGA-EQ-8122 TCGA-F1-6875 TCGA-FP-7735 TCGA-FP-8631 TCGA-IN-7808 
        7.79        72.23         0.39         0.56         3.55 

$`1Q GAIN WILD-TYPE`
TCGA-B7-5816 TCGA-B7-5818 TCGA-BR-6452 TCGA-BR-6455 TCGA-BR-6457 TCGA-BR-6458 
        5.62         0.10         0.95         1.41         1.35         1.35 
TCGA-BR-6563 TCGA-BR-6564 TCGA-BR-6565 TCGA-BR-6566 TCGA-BR-6705 TCGA-BR-6706 
        0.85         0.82         0.62         0.62         1.71         2.17 
TCGA-BR-6707 TCGA-BR-6709 TCGA-BR-6710 TCGA-BR-6801 TCGA-BR-6802 TCGA-BR-6803 
        0.99         1.22         0.66         1.12         0.76         0.66 
TCGA-BR-6852 TCGA-BR-7196 TCGA-BR-7197 TCGA-BR-7703 TCGA-BR-7704 TCGA-BR-7707 
        0.26         1.22         1.48         0.46         1.25         0.13 
TCGA-BR-7715 TCGA-BR-7716 TCGA-BR-7722 TCGA-BR-7851 TCGA-BR-7901 TCGA-BR-7957 
        1.05         0.82         0.16         0.99         0.95         0.69 
TCGA-BR-7958 TCGA-BR-7959 TCGA-BR-8059 TCGA-BR-8060 TCGA-BR-8077 TCGA-BR-8078 
        0.16         1.08         0.82         1.32         0.69         0.95 
TCGA-BR-8080 TCGA-BR-8081 TCGA-BR-8284 TCGA-BR-8285 TCGA-BR-8289 TCGA-BR-8291 
        0.49         0.46         0.72         0.26         0.26         1.18 
TCGA-BR-8296 TCGA-BR-8297 TCGA-BR-8592 TCGA-BR-A4IU TCGA-BR-A4IV TCGA-BR-A4IY 
        1.48         0.76         0.20         0.59         0.92         0.39 
TCGA-BR-A4IZ TCGA-BR-A4J1 TCGA-BR-A4J2 TCGA-BR-A4J4 TCGA-BR-A4J5 TCGA-BR-A4J6 
        0.79         0.72         0.79         0.53         0.43         0.13 
TCGA-BR-A4J9 TCGA-BR-A4PF TCGA-BR-A4QI TCGA-BR-A4QL TCGA-CD-5798 TCGA-CD-5799 
        0.10         0.72         0.49         2.24         0.82         0.69 
TCGA-CD-5800 TCGA-CD-5801 TCGA-CD-5802 TCGA-CD-5803 TCGA-CG-4300 TCGA-CG-4301 
        0.36         0.49         0.30         0.07        20.02         3.02 
TCGA-CG-4304 TCGA-CG-4305 TCGA-CG-4306 TCGA-CG-4436 TCGA-CG-4437 TCGA-CG-4438 
       27.02        15.95         1.02        52.96         8.05        54.05 
TCGA-CG-4440 TCGA-CG-4441 TCGA-CG-4443 TCGA-CG-4444 TCGA-CG-4449 TCGA-CG-4455 
        4.01        14.01        29.98        47.05        19.07        12.03 
TCGA-CG-4462 TCGA-CG-4465 TCGA-CG-4466 TCGA-CG-4469 TCGA-CG-4472 TCGA-CG-4474 
        1.02         8.98        18.94         7.07        12.00         1.02 
TCGA-CG-4477 TCGA-CG-5716 TCGA-CG-5717 TCGA-CG-5718 TCGA-CG-5719 TCGA-CG-5720 
        1.02         1.02         6.94         1.02         1.02         0.99 
TCGA-CG-5721 TCGA-CG-5722 TCGA-CG-5723 TCGA-CG-5724 TCGA-CG-5725 TCGA-CG-5726 
        5.98         0.95        70.06        12.03        15.02        28.96 
TCGA-CG-5727 TCGA-CG-5728 TCGA-CG-5730 TCGA-CG-5732 TCGA-CG-5733 TCGA-CG-5734 
       31.04        65.10         4.01        55.04        21.07         7.99 
TCGA-D7-5577 TCGA-D7-5578 TCGA-D7-5579 TCGA-D7-6518 TCGA-D7-6519 TCGA-D7-6520 
        8.65         3.58         4.54         9.80        15.65         9.63 
TCGA-D7-6521 TCGA-D7-6522 TCGA-D7-6524 TCGA-D7-6525 TCGA-D7-6528 TCGA-D7-6815 
        8.19         6.90         0.69         5.95         1.68         3.65 
TCGA-D7-6820 TCGA-F1-6177 TCGA-F1-6874 TCGA-FP-7829 TCGA-FP-7916 TCGA-FP-7998 
        2.93         6.54         2.01         0.20         3.02         3.58 
TCGA-FP-8099 TCGA-FP-8209 TCGA-FP-8210 TCGA-HJ-7597 TCGA-IN-7806 TCGA-IP-7968 
        1.02        59.05         5.03        26.43         6.87         2.53 

      1Q GAIN CNV 1Q GAIN WILD-TYPE 
             0.23              0.07 
      1Q GAIN CNV 1Q GAIN WILD-TYPE 
            72.23             70.06 
      1Q GAIN CNV 1Q GAIN WILD-TYPE 
             4.04              1.20 
[1] "0.2 - 72.2 (4.0)" "0.1 - 70.1 (1.2)"
       TCGA-B7-5816        TCGA-B7-5818        TCGA-BR-6452        TCGA-BR-6455 
"1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" 
       TCGA-BR-6457        TCGA-BR-6458        TCGA-BR-6563        TCGA-BR-6564 
"1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" 
       TCGA-BR-6565        TCGA-BR-6566        TCGA-BR-6705        TCGA-BR-6706 
"1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" 
       TCGA-BR-6707        TCGA-BR-6709        TCGA-BR-6710        TCGA-BR-6801 
"1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" 
       TCGA-BR-6802        TCGA-BR-6803        TCGA-BR-6852        TCGA-BR-7196 
"1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" 
       TCGA-BR-7197        TCGA-BR-7703        TCGA-BR-7704        TCGA-BR-7707 
"1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" 
       TCGA-BR-7715        TCGA-BR-7716        TCGA-BR-7717        TCGA-BR-7722 
"1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE"       "1Q GAIN CNV" "1Q GAIN WILD-TYPE" 
       TCGA-BR-7723        TCGA-BR-7851        TCGA-BR-7901        TCGA-BR-7957 
      "1Q GAIN CNV" "1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" 
       TCGA-BR-7958        TCGA-BR-7959        TCGA-BR-8059        TCGA-BR-8060 
"1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" 
       TCGA-BR-8077        TCGA-BR-8078        TCGA-BR-8080        TCGA-BR-8081 
"1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" 
       TCGA-BR-8284        TCGA-BR-8285        TCGA-BR-8286        TCGA-BR-8289 
"1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE"       "1Q GAIN CNV" "1Q GAIN WILD-TYPE" 
       TCGA-BR-8291        TCGA-BR-8295        TCGA-BR-8296        TCGA-BR-8297 
"1Q GAIN WILD-TYPE"       "1Q GAIN CNV" "1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" 
       TCGA-BR-8592        TCGA-BR-A4IU        TCGA-BR-A4IV        TCGA-BR-A4IY 
"1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" 
       TCGA-BR-A4IZ        TCGA-BR-A4J1        TCGA-BR-A4J2        TCGA-BR-A4J4 
"1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" 
       TCGA-BR-A4J5        TCGA-BR-A4J6        TCGA-BR-A4J8        TCGA-BR-A4J9 
"1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE"       "1Q GAIN CNV" "1Q GAIN WILD-TYPE" 
       TCGA-BR-A4PF        TCGA-BR-A4QI        TCGA-BR-A4QL        TCGA-CD-5798 
"1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" 
       TCGA-CD-5799        TCGA-CD-5800        TCGA-CD-5801        TCGA-CD-5802 
"1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" 
       TCGA-CD-5803        TCGA-CG-4300        TCGA-CG-4301        TCGA-CG-4304 
"1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" 
       TCGA-CG-4305        TCGA-CG-4306        TCGA-CG-4436        TCGA-CG-4437 
"1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" 
       TCGA-CG-4438        TCGA-CG-4440        TCGA-CG-4441        TCGA-CG-4443 
"1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" 
       TCGA-CG-4444        TCGA-CG-4449        TCGA-CG-4455        TCGA-CG-4460 
"1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE"       "1Q GAIN CNV" 
       TCGA-CG-4462        TCGA-CG-4465        TCGA-CG-4466        TCGA-CG-4469 
"1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" 
       TCGA-CG-4472        TCGA-CG-4474        TCGA-CG-4477        TCGA-CG-5716 
"1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" 
       TCGA-CG-5717        TCGA-CG-5718        TCGA-CG-5719        TCGA-CG-5720 
"1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" 
       TCGA-CG-5721        TCGA-CG-5722        TCGA-CG-5723        TCGA-CG-5724 
"1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" 
       TCGA-CG-5725        TCGA-CG-5726        TCGA-CG-5727        TCGA-CG-5728 
"1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" 
       TCGA-CG-5730        TCGA-CG-5732        TCGA-CG-5733        TCGA-CG-5734 
"1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" 
       TCGA-D7-5577        TCGA-D7-5578        TCGA-D7-5579        TCGA-D7-6518 
"1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" 
       TCGA-D7-6519        TCGA-D7-6520        TCGA-D7-6521        TCGA-D7-6522 
"1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" 
       TCGA-D7-6524        TCGA-D7-6525        TCGA-D7-6526        TCGA-D7-6527 
"1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE"       "1Q GAIN CNV"       "1Q GAIN CNV" 
       TCGA-D7-6528        TCGA-D7-6815        TCGA-D7-6817        TCGA-D7-6818 
"1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE"       "1Q GAIN CNV"       "1Q GAIN CNV" 
       TCGA-D7-6820        TCGA-D7-6822        TCGA-EQ-5647        TCGA-EQ-8122 
"1Q GAIN WILD-TYPE"       "1Q GAIN CNV"       "1Q GAIN CNV"       "1Q GAIN CNV" 
       TCGA-F1-6177        TCGA-F1-6874        TCGA-F1-6875        TCGA-FP-7735 
"1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE"       "1Q GAIN CNV"       "1Q GAIN CNV" 
       TCGA-FP-7829        TCGA-FP-7916        TCGA-FP-7998        TCGA-FP-8099 
"1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" 
       TCGA-FP-8209        TCGA-FP-8210        TCGA-FP-8631        TCGA-HJ-7597 
"1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE"       "1Q GAIN CNV" "1Q GAIN WILD-TYPE" 
       TCGA-IN-7806        TCGA-IN-7808        TCGA-IP-7968 
"1Q GAIN WILD-TYPE"       "1Q GAIN CNV" "1Q GAIN WILD-TYPE" 
       TCGA-B7-5816        TCGA-B7-5818        TCGA-BR-6452        TCGA-BR-6455 
"1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" 
       TCGA-BR-6457        TCGA-BR-6458        TCGA-BR-6563        TCGA-BR-6564 
"1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" 
       TCGA-BR-6565        TCGA-BR-6566        TCGA-BR-6705        TCGA-BR-6706 
"1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" 
       TCGA-BR-6707        TCGA-BR-6709        TCGA-BR-6710        TCGA-BR-6801 
"1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" 
       TCGA-BR-6802        TCGA-BR-6803        TCGA-BR-6852        TCGA-BR-7196 
"1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" 
       TCGA-BR-7197        TCGA-BR-7703        TCGA-BR-7704        TCGA-BR-7707 
"1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" 
       TCGA-BR-7715        TCGA-BR-7716        TCGA-BR-7717        TCGA-BR-7722 
"1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE"       "1Q GAIN CNV" "1Q GAIN WILD-TYPE" 
       TCGA-BR-7723        TCGA-BR-7851        TCGA-BR-7901        TCGA-BR-7957 
      "1Q GAIN CNV" "1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" 
       TCGA-BR-7958        TCGA-BR-7959        TCGA-BR-8059        TCGA-BR-8060 
"1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" 
       TCGA-BR-8077        TCGA-BR-8078        TCGA-BR-8080        TCGA-BR-8081 
"1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" 
       TCGA-BR-8284        TCGA-BR-8285        TCGA-BR-8286        TCGA-BR-8289 
"1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE"       "1Q GAIN CNV" "1Q GAIN WILD-TYPE" 
       TCGA-BR-8291        TCGA-BR-8295        TCGA-BR-8296        TCGA-BR-8297 
"1Q GAIN WILD-TYPE"       "1Q GAIN CNV" "1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" 
       TCGA-BR-8592        TCGA-BR-A4IU        TCGA-BR-A4IV        TCGA-BR-A4IY 
"1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" 
       TCGA-BR-A4IZ        TCGA-BR-A4J1        TCGA-BR-A4J2        TCGA-BR-A4J4 
"1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" 
       TCGA-BR-A4J5        TCGA-BR-A4J6        TCGA-BR-A4J8        TCGA-BR-A4J9 
"1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE"       "1Q GAIN CNV" "1Q GAIN WILD-TYPE" 
       TCGA-BR-A4PF        TCGA-BR-A4QI        TCGA-BR-A4QL        TCGA-CD-5798 
"1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" 
       TCGA-CD-5799        TCGA-CD-5800        TCGA-CD-5801        TCGA-CD-5802 
"1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" 
       TCGA-CD-5803        TCGA-CG-4300        TCGA-CG-4301        TCGA-CG-4304 
"1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" 
       TCGA-CG-4305        TCGA-CG-4306        TCGA-CG-4436        TCGA-CG-4437 
"1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" 
       TCGA-CG-4438        TCGA-CG-4440        TCGA-CG-4441        TCGA-CG-4443 
"1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" 
       TCGA-CG-4444        TCGA-CG-4449        TCGA-CG-4455        TCGA-CG-4460 
"1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE"       "1Q GAIN CNV" 
       TCGA-CG-4462        TCGA-CG-4465        TCGA-CG-4466        TCGA-CG-4469 
"1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" 
       TCGA-CG-4472        TCGA-CG-4474        TCGA-CG-4477        TCGA-CG-5716 
"1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" 
       TCGA-CG-5717        TCGA-CG-5718        TCGA-CG-5719        TCGA-CG-5720 
"1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" 
       TCGA-CG-5721        TCGA-CG-5722        TCGA-CG-5723        TCGA-CG-5724 
"1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" 
       TCGA-CG-5725        TCGA-CG-5726        TCGA-CG-5727        TCGA-CG-5728 
"1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" 
       TCGA-CG-5730        TCGA-CG-5732        TCGA-CG-5733        TCGA-CG-5734 
"1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" 
       TCGA-D7-5577        TCGA-D7-5578        TCGA-D7-5579        TCGA-D7-6518 
"1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" 
       TCGA-D7-6519        TCGA-D7-6520        TCGA-D7-6521        TCGA-D7-6522 
"1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" 
       TCGA-D7-6524        TCGA-D7-6525        TCGA-D7-6526        TCGA-D7-6527 
"1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE"       "1Q GAIN CNV"       "1Q GAIN CNV" 
       TCGA-D7-6528        TCGA-D7-6815        TCGA-D7-6817        TCGA-D7-6818 
"1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE"       "1Q GAIN CNV"       "1Q GAIN CNV" 
       TCGA-D7-6820        TCGA-D7-6822        TCGA-EQ-5647        TCGA-EQ-8122 
"1Q GAIN WILD-TYPE"       "1Q GAIN CNV"       "1Q GAIN CNV"       "1Q GAIN CNV" 
       TCGA-F1-6177        TCGA-F1-6874        TCGA-F1-6875        TCGA-FP-7735 
"1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE"       "1Q GAIN CNV"       "1Q GAIN CNV" 
       TCGA-FP-7829        TCGA-FP-7916        TCGA-FP-7998        TCGA-FP-8099 
"1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" 
       TCGA-FP-8209        TCGA-FP-8210        TCGA-FP-8631        TCGA-HJ-7597 
"1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE"       "1Q GAIN CNV" "1Q GAIN WILD-TYPE" 
       TCGA-IN-7806        TCGA-IN-7808        TCGA-IP-7968 
"1Q GAIN WILD-TYPE"       "1Q GAIN CNV" "1Q GAIN WILD-TYPE" 
       TCGA-B7-5816        TCGA-B7-5818        TCGA-BR-6452        TCGA-BR-6455 
"1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" 
       TCGA-BR-6457        TCGA-BR-6458        TCGA-BR-6563        TCGA-BR-6564 
"1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" 
       TCGA-BR-6565        TCGA-BR-6566        TCGA-BR-6705        TCGA-BR-6706 
"1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" 
       TCGA-BR-6707        TCGA-BR-6709        TCGA-BR-6710        TCGA-BR-6801 
"1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" 
       TCGA-BR-6802        TCGA-BR-6803        TCGA-BR-6852        TCGA-BR-7196 
"1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" 
       TCGA-BR-7197        TCGA-BR-7703        TCGA-BR-7704        TCGA-BR-7707 
"1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" 
       TCGA-BR-7715        TCGA-BR-7716        TCGA-BR-7717        TCGA-BR-7722 
"1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE"       "1Q GAIN CNV" "1Q GAIN WILD-TYPE" 
       TCGA-BR-7723        TCGA-BR-7851        TCGA-BR-7901        TCGA-BR-7957 
      "1Q GAIN CNV" "1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" 
       TCGA-BR-7958        TCGA-BR-7959        TCGA-BR-8059        TCGA-BR-8060 
"1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" 
       TCGA-BR-8077        TCGA-BR-8078        TCGA-BR-8080        TCGA-BR-8081 
"1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" 
       TCGA-BR-8284        TCGA-BR-8285        TCGA-BR-8286        TCGA-BR-8289 
"1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE"       "1Q GAIN CNV" "1Q GAIN WILD-TYPE" 
       TCGA-BR-8291        TCGA-BR-8295        TCGA-BR-8296        TCGA-BR-8297 
"1Q GAIN WILD-TYPE"       "1Q GAIN CNV" "1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" 
       TCGA-BR-8592        TCGA-BR-A4IU        TCGA-BR-A4IV        TCGA-BR-A4IY 
"1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" 
       TCGA-BR-A4IZ        TCGA-BR-A4J1        TCGA-BR-A4J2        TCGA-BR-A4J4 
"1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" 
       TCGA-BR-A4J5        TCGA-BR-A4J6        TCGA-BR-A4J8        TCGA-BR-A4J9 
"1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE"       "1Q GAIN CNV" "1Q GAIN WILD-TYPE" 
       TCGA-BR-A4PF        TCGA-BR-A4QI        TCGA-BR-A4QL        TCGA-CD-5798 
"1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" 
       TCGA-CD-5799        TCGA-CD-5800        TCGA-CD-5801        TCGA-CD-5802 
"1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" 
       TCGA-CD-5803        TCGA-CG-4300        TCGA-CG-4301        TCGA-CG-4304 
"1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" 
       TCGA-CG-4305        TCGA-CG-4306        TCGA-CG-4436        TCGA-CG-4437 
"1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" 
       TCGA-CG-4438        TCGA-CG-4440        TCGA-CG-4441        TCGA-CG-4443 
"1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" 
       TCGA-CG-4444        TCGA-CG-4449        TCGA-CG-4455        TCGA-CG-4460 
"1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE"       "1Q GAIN CNV" 
       TCGA-CG-4462        TCGA-CG-4465        TCGA-CG-4466        TCGA-CG-4469 
"1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" 
       TCGA-CG-4472        TCGA-CG-4474        TCGA-CG-4477        TCGA-CG-5716 
"1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" 
       TCGA-CG-5717        TCGA-CG-5718        TCGA-CG-5719        TCGA-CG-5720 
"1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" 
       TCGA-CG-5721        TCGA-CG-5722        TCGA-CG-5723        TCGA-CG-5724 
"1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" 
       TCGA-CG-5725        TCGA-CG-5726        TCGA-CG-5727        TCGA-CG-5728 
"1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" 
       TCGA-CG-5730        TCGA-CG-5732        TCGA-CG-5733        TCGA-CG-5734 
"1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" 
       TCGA-D7-5577        TCGA-D7-5578        TCGA-D7-5579        TCGA-D7-6518 
"1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" 
       TCGA-D7-6519        TCGA-D7-6520        TCGA-D7-6521        TCGA-D7-6522 
"1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" 
       TCGA-D7-6524        TCGA-D7-6525        TCGA-D7-6526        TCGA-D7-6527 
"1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE"       "1Q GAIN CNV"       "1Q GAIN CNV" 
       TCGA-D7-6528        TCGA-D7-6815        TCGA-D7-6817        TCGA-D7-6818 
"1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE"       "1Q GAIN CNV"       "1Q GAIN CNV" 
       TCGA-D7-6820        TCGA-D7-6822        TCGA-EQ-5647        TCGA-EQ-8122 
"1Q GAIN WILD-TYPE"       "1Q GAIN CNV"       "1Q GAIN CNV"       "1Q GAIN CNV" 
       TCGA-F1-6177        TCGA-F1-6874        TCGA-F1-6875        TCGA-FP-7735 
"1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE"       "1Q GAIN CNV"       "1Q GAIN CNV" 
       TCGA-FP-7829        TCGA-FP-7916        TCGA-FP-7998        TCGA-FP-8099 
"1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" 
       TCGA-FP-8209        TCGA-FP-8210        TCGA-FP-8631        TCGA-HJ-7597 
"1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE"       "1Q GAIN CNV" "1Q GAIN WILD-TYPE" 
       TCGA-IN-7806        TCGA-IN-7808        TCGA-IP-7968 
"1Q GAIN WILD-TYPE"       "1Q GAIN CNV" "1Q GAIN WILD-TYPE" 
[1] "hr=" "1"  
D2V2, continuous
D2V3, binary
[1] "tbl2"
                   cls
clus                [,1] [,2]
  1Q GAIN CNV          8   17
  1Q GAIN WILD-TYPE   64   91
        clus
vv       1Q GAIN CNV 1Q GAIN WILD-TYPE
  FEMALE           8                64
  MALE            17                91
                   vv
clus                STOMACH  ADENOCARCINOMA  DIFFUSE TYPE
  1Q GAIN CNV                                           0
  1Q GAIN WILD-TYPE                                    10
                   vv
clus                STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  1Q GAIN CNV                                                            3
  1Q GAIN WILD-TYPE                                                     13
                   vv
clus                STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  1Q GAIN CNV                                                                       2
  1Q GAIN WILD-TYPE                                                                 6
                   vv
clus                STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE
  1Q GAIN CNV                                                              0
  1Q GAIN WILD-TYPE                                                        3
                   vv
clus                STOMACH ADENOCARCINOMA  SIGNET RING TYPE
  1Q GAIN CNV                                              0
  1Q GAIN WILD-TYPE                                        1
                   vv
clus                STOMACH ADENOCARCINOMA - DIFFUSE TYPE
  1Q GAIN CNV                                           2
  1Q GAIN WILD-TYPE                                    14
                   vv
clus                STOMACH ADENOCARCINOMA - NOT OTHERWISE SPECIFIED (NOS)
  1Q GAIN CNV                                                           12
  1Q GAIN WILD-TYPE                                                     61
                   vv
clus                STOMACH INTESTINAL ADENOCARCINOMA - MUCINOUS TYPE
  1Q GAIN CNV                                                       0
  1Q GAIN WILD-TYPE                                                 7
                   vv
clus                STOMACH INTESTINAL ADENOCARCINOMA - PAPILLARY TYPE
  1Q GAIN CNV                                                        1
  1Q GAIN WILD-TYPE                                                  2
                   vv
clus                STOMACH INTESTINAL ADENOCARCINOMA - TUBULAR TYPE
  1Q GAIN CNV                                                      3
  1Q GAIN WILD-TYPE                                                7
                   vv
clus                STOMACH INTESTINAL ADENOCARCINOMA - TYPE NOT OTHERWISE SPECIFIED (NOS)
  1Q GAIN CNV                                                                            2
  1Q GAIN WILD-TYPE                                                                     26
D2V4, multiclass
                   vv
clus                T1 T2 T3 T4
  1Q GAIN CNV        1  8  6  3
  1Q GAIN WILD-TYPE  5 44 50 15
D2V5, multiclass
    clus
vv   1Q GAIN CNV 1Q GAIN WILD-TYPE
  T1           1                 5
  T2           8                44
  T3           6                50
  T4           3                15
                   vv
clus                N0 N1 N2 N3
  1Q GAIN CNV        6  4  2  4
  1Q GAIN WILD-TYPE 38 45 21 11
D2V6, multiclass
    clus
vv   1Q GAIN CNV 1Q GAIN WILD-TYPE
  N0           6                38
  N1           4                45
  N2           2                21
  N3           4                11
                   vv
clus                 M0  M1  MX
  1Q GAIN CNV        15   3   2
  1Q GAIN WILD-TYPE 103  13   6
D2V7, multiclass
    clus
vv   1Q GAIN CNV 1Q GAIN WILD-TYPE
  M0          15               103
  M1           3                13
  MX           2                 6
                   vv
clus                 I II III IV
  1Q GAIN CNV        5  3   4  4
  1Q GAIN WILD-TYPE 19 34  35 22
D2V8, multiclass
     clus
vv    1Q GAIN CNV 1Q GAIN WILD-TYPE
  I             5                19
  II            3                34
  III           4                35
  IV            4                22
D2V9, binary
[1] "tbl2"
                   cls
clus                [,1] [,2]
  1Q GAIN CNV          2   23
  1Q GAIN WILD-TYPE    3  152
     clus
vv    1Q GAIN CNV 1Q GAIN WILD-TYPE
  NO            2                 3
  YES          23               152
                   vv
clus                 R0  R1  R2  RX
  1Q GAIN CNV        16   0   2   5
  1Q GAIN WILD-TYPE 109   7  10  20
D2V10, multiclass
    clus
vv   1Q GAIN CNV 1Q GAIN WILD-TYPE
  R0          16               109
  R1           0                 7
  R2           2                10
  RX           5                20
D2V11, continuous

Clustering(3) Variable = 2p gain
D3V1, survival
                   sevent
clus2                 0   1
  2P GAIN CNV        11   1
  2P GAIN WILD-TYPE 113  18
      2P GAIN CNV 2P GAIN WILD-TYPE 
               12               131 
      2P GAIN CNV 2P GAIN WILD-TYPE 
                1                18 
$`2P GAIN CNV`
TCGA-BR-7197 TCGA-BR-7704 TCGA-BR-7715 TCGA-BR-7717 TCGA-BR-8295 TCGA-BR-A4IY 
        1.48         1.25         1.05         0.69         1.55         0.39 
TCGA-CD-5801 TCGA-CD-5802 TCGA-CG-4460 TCGA-CG-4472 TCGA-CG-5718 TCGA-CG-5727 
        0.49         0.30        21.99        12.00         1.02        31.04 

$`2P GAIN WILD-TYPE`
TCGA-B7-5816 TCGA-B7-5818 TCGA-BR-6452 TCGA-BR-6455 TCGA-BR-6457 TCGA-BR-6458 
        5.62         0.10         0.95         1.41         1.35         1.35 
TCGA-BR-6563 TCGA-BR-6564 TCGA-BR-6565 TCGA-BR-6566 TCGA-BR-6705 TCGA-BR-6706 
        0.85         0.82         0.62         0.62         1.71         2.17 
TCGA-BR-6707 TCGA-BR-6709 TCGA-BR-6710 TCGA-BR-6801 TCGA-BR-6802 TCGA-BR-6803 
        0.99         1.22         0.66         1.12         0.76         0.66 
TCGA-BR-6852 TCGA-BR-7196 TCGA-BR-7703 TCGA-BR-7707 TCGA-BR-7716 TCGA-BR-7722 
        0.26         1.22         0.46         0.13         0.82         0.16 
TCGA-BR-7723 TCGA-BR-7851 TCGA-BR-7901 TCGA-BR-7957 TCGA-BR-7958 TCGA-BR-7959 
        4.54         0.99         0.95         0.69         0.16         1.08 
TCGA-BR-8059 TCGA-BR-8060 TCGA-BR-8077 TCGA-BR-8078 TCGA-BR-8080 TCGA-BR-8081 
        0.82         1.32         0.69         0.95         0.49         0.46 
TCGA-BR-8284 TCGA-BR-8285 TCGA-BR-8286 TCGA-BR-8289 TCGA-BR-8291 TCGA-BR-8296 
        0.72         0.26         0.43         0.26         1.18         1.48 
TCGA-BR-8297 TCGA-BR-8592 TCGA-BR-A4IU TCGA-BR-A4IV TCGA-BR-A4IZ TCGA-BR-A4J1 
        0.76         0.20         0.59         0.92         0.79         0.72 
TCGA-BR-A4J2 TCGA-BR-A4J4 TCGA-BR-A4J5 TCGA-BR-A4J6 TCGA-BR-A4J8 TCGA-BR-A4J9 
        0.79         0.53         0.43         0.13         0.23         0.10 
TCGA-BR-A4PF TCGA-BR-A4QI TCGA-BR-A4QL TCGA-CD-5798 TCGA-CD-5799 TCGA-CD-5800 
        0.72         0.49         2.24         0.82         0.69         0.36 
TCGA-CD-5803 TCGA-CG-4300 TCGA-CG-4301 TCGA-CG-4304 TCGA-CG-4305 TCGA-CG-4306 
        0.07        20.02         3.02        27.02        15.95         1.02 
TCGA-CG-4436 TCGA-CG-4437 TCGA-CG-4438 TCGA-CG-4440 TCGA-CG-4441 TCGA-CG-4443 
       52.96         8.05        54.05         4.01        14.01        29.98 
TCGA-CG-4444 TCGA-CG-4449 TCGA-CG-4455 TCGA-CG-4462 TCGA-CG-4465 TCGA-CG-4466 
       47.05        19.07        12.03         1.02         8.98        18.94 
TCGA-CG-4469 TCGA-CG-4474 TCGA-CG-4477 TCGA-CG-5716 TCGA-CG-5717 TCGA-CG-5719 
        7.07         1.02         1.02         1.02         6.94         1.02 
TCGA-CG-5720 TCGA-CG-5721 TCGA-CG-5722 TCGA-CG-5723 TCGA-CG-5724 TCGA-CG-5725 
        0.99         5.98         0.95        70.06        12.03        15.02 
TCGA-CG-5726 TCGA-CG-5728 TCGA-CG-5730 TCGA-CG-5732 TCGA-CG-5733 TCGA-CG-5734 
       28.96        65.10         4.01        55.04        21.07         7.99 
TCGA-D7-5577 TCGA-D7-5578 TCGA-D7-5579 TCGA-D7-6518 TCGA-D7-6519 TCGA-D7-6520 
        8.65         3.58         4.54         9.80        15.65         9.63 
TCGA-D7-6521 TCGA-D7-6522 TCGA-D7-6524 TCGA-D7-6525 TCGA-D7-6526 TCGA-D7-6527 
        8.19         6.90         0.69         5.95         6.61         4.14 
TCGA-D7-6528 TCGA-D7-6815 TCGA-D7-6817 TCGA-D7-6818 TCGA-D7-6820 TCGA-D7-6822 
        1.68         3.65         4.70         4.04         2.93         4.27 
TCGA-EQ-5647 TCGA-EQ-8122 TCGA-F1-6177 TCGA-F1-6874 TCGA-F1-6875 TCGA-FP-7735 
        0.62         7.79         6.54         2.01        72.23         0.39 
TCGA-FP-7829 TCGA-FP-7916 TCGA-FP-7998 TCGA-FP-8099 TCGA-FP-8209 TCGA-FP-8210 
        0.20         3.02         3.58         1.02        59.05         5.03 
TCGA-FP-8631 TCGA-HJ-7597 TCGA-IN-7806 TCGA-IN-7808 TCGA-IP-7968 
        0.56        26.43         6.87         3.55         2.53 

      2P GAIN CNV 2P GAIN WILD-TYPE 
             0.30              0.07 
      2P GAIN CNV 2P GAIN WILD-TYPE 
            31.04             72.23 
      2P GAIN CNV 2P GAIN WILD-TYPE 
             1.15              1.32 
[1] "0.3 - 31.0 (1.1)" "0.1 - 72.2 (1.3)"
       TCGA-B7-5816        TCGA-B7-5818        TCGA-BR-6452        TCGA-BR-6455 
"2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" 
       TCGA-BR-6457        TCGA-BR-6458        TCGA-BR-6563        TCGA-BR-6564 
"2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" 
       TCGA-BR-6565        TCGA-BR-6566        TCGA-BR-6705        TCGA-BR-6706 
"2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" 
       TCGA-BR-6707        TCGA-BR-6709        TCGA-BR-6710        TCGA-BR-6801 
"2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" 
       TCGA-BR-6802        TCGA-BR-6803        TCGA-BR-6852        TCGA-BR-7196 
"2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" 
       TCGA-BR-7197        TCGA-BR-7703        TCGA-BR-7704        TCGA-BR-7707 
      "2P GAIN CNV" "2P GAIN WILD-TYPE"       "2P GAIN CNV" "2P GAIN WILD-TYPE" 
       TCGA-BR-7715        TCGA-BR-7716        TCGA-BR-7717        TCGA-BR-7722 
      "2P GAIN CNV" "2P GAIN WILD-TYPE"       "2P GAIN CNV" "2P GAIN WILD-TYPE" 
       TCGA-BR-7723        TCGA-BR-7851        TCGA-BR-7901        TCGA-BR-7957 
"2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" 
       TCGA-BR-7958        TCGA-BR-7959        TCGA-BR-8059        TCGA-BR-8060 
"2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" 
       TCGA-BR-8077        TCGA-BR-8078        TCGA-BR-8080        TCGA-BR-8081 
"2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" 
       TCGA-BR-8284        TCGA-BR-8285        TCGA-BR-8286        TCGA-BR-8289 
"2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" 
       TCGA-BR-8291        TCGA-BR-8295        TCGA-BR-8296        TCGA-BR-8297 
"2P GAIN WILD-TYPE"       "2P GAIN CNV" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" 
       TCGA-BR-8592        TCGA-BR-A4IU        TCGA-BR-A4IV        TCGA-BR-A4IY 
"2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE"       "2P GAIN CNV" 
       TCGA-BR-A4IZ        TCGA-BR-A4J1        TCGA-BR-A4J2        TCGA-BR-A4J4 
"2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" 
       TCGA-BR-A4J5        TCGA-BR-A4J6        TCGA-BR-A4J8        TCGA-BR-A4J9 
"2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" 
       TCGA-BR-A4PF        TCGA-BR-A4QI        TCGA-BR-A4QL        TCGA-CD-5798 
"2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" 
       TCGA-CD-5799        TCGA-CD-5800        TCGA-CD-5801        TCGA-CD-5802 
"2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE"       "2P GAIN CNV"       "2P GAIN CNV" 
       TCGA-CD-5803        TCGA-CG-4300        TCGA-CG-4301        TCGA-CG-4304 
"2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" 
       TCGA-CG-4305        TCGA-CG-4306        TCGA-CG-4436        TCGA-CG-4437 
"2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" 
       TCGA-CG-4438        TCGA-CG-4440        TCGA-CG-4441        TCGA-CG-4443 
"2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" 
       TCGA-CG-4444        TCGA-CG-4449        TCGA-CG-4455        TCGA-CG-4460 
"2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE"       "2P GAIN CNV" 
       TCGA-CG-4462        TCGA-CG-4465        TCGA-CG-4466        TCGA-CG-4469 
"2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" 
       TCGA-CG-4472        TCGA-CG-4474        TCGA-CG-4477        TCGA-CG-5716 
      "2P GAIN CNV" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" 
       TCGA-CG-5717        TCGA-CG-5718        TCGA-CG-5719        TCGA-CG-5720 
"2P GAIN WILD-TYPE"       "2P GAIN CNV" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" 
       TCGA-CG-5721        TCGA-CG-5722        TCGA-CG-5723        TCGA-CG-5724 
"2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" 
       TCGA-CG-5725        TCGA-CG-5726        TCGA-CG-5727        TCGA-CG-5728 
"2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE"       "2P GAIN CNV" "2P GAIN WILD-TYPE" 
       TCGA-CG-5730        TCGA-CG-5732        TCGA-CG-5733        TCGA-CG-5734 
"2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" 
       TCGA-D7-5577        TCGA-D7-5578        TCGA-D7-5579        TCGA-D7-6518 
"2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" 
       TCGA-D7-6519        TCGA-D7-6520        TCGA-D7-6521        TCGA-D7-6522 
"2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" 
       TCGA-D7-6524        TCGA-D7-6525        TCGA-D7-6526        TCGA-D7-6527 
"2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" 
       TCGA-D7-6528        TCGA-D7-6815        TCGA-D7-6817        TCGA-D7-6818 
"2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" 
       TCGA-D7-6820        TCGA-D7-6822        TCGA-EQ-5647        TCGA-EQ-8122 
"2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" 
       TCGA-F1-6177        TCGA-F1-6874        TCGA-F1-6875        TCGA-FP-7735 
"2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" 
       TCGA-FP-7829        TCGA-FP-7916        TCGA-FP-7998        TCGA-FP-8099 
"2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" 
       TCGA-FP-8209        TCGA-FP-8210        TCGA-FP-8631        TCGA-HJ-7597 
"2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" 
       TCGA-IN-7806        TCGA-IN-7808        TCGA-IP-7968 
"2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" 
       TCGA-B7-5816        TCGA-B7-5818        TCGA-BR-6452        TCGA-BR-6455 
"2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" 
       TCGA-BR-6457        TCGA-BR-6458        TCGA-BR-6563        TCGA-BR-6564 
"2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" 
       TCGA-BR-6565        TCGA-BR-6566        TCGA-BR-6705        TCGA-BR-6706 
"2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" 
       TCGA-BR-6707        TCGA-BR-6709        TCGA-BR-6710        TCGA-BR-6801 
"2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" 
       TCGA-BR-6802        TCGA-BR-6803        TCGA-BR-6852        TCGA-BR-7196 
"2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" 
       TCGA-BR-7197        TCGA-BR-7703        TCGA-BR-7704        TCGA-BR-7707 
      "2P GAIN CNV" "2P GAIN WILD-TYPE"       "2P GAIN CNV" "2P GAIN WILD-TYPE" 
       TCGA-BR-7715        TCGA-BR-7716        TCGA-BR-7717        TCGA-BR-7722 
      "2P GAIN CNV" "2P GAIN WILD-TYPE"       "2P GAIN CNV" "2P GAIN WILD-TYPE" 
       TCGA-BR-7723        TCGA-BR-7851        TCGA-BR-7901        TCGA-BR-7957 
"2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" 
       TCGA-BR-7958        TCGA-BR-7959        TCGA-BR-8059        TCGA-BR-8060 
"2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" 
       TCGA-BR-8077        TCGA-BR-8078        TCGA-BR-8080        TCGA-BR-8081 
"2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" 
       TCGA-BR-8284        TCGA-BR-8285        TCGA-BR-8286        TCGA-BR-8289 
"2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" 
       TCGA-BR-8291        TCGA-BR-8295        TCGA-BR-8296        TCGA-BR-8297 
"2P GAIN WILD-TYPE"       "2P GAIN CNV" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" 
       TCGA-BR-8592        TCGA-BR-A4IU        TCGA-BR-A4IV        TCGA-BR-A4IY 
"2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE"       "2P GAIN CNV" 
       TCGA-BR-A4IZ        TCGA-BR-A4J1        TCGA-BR-A4J2        TCGA-BR-A4J4 
"2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" 
       TCGA-BR-A4J5        TCGA-BR-A4J6        TCGA-BR-A4J8        TCGA-BR-A4J9 
"2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" 
       TCGA-BR-A4PF        TCGA-BR-A4QI        TCGA-BR-A4QL        TCGA-CD-5798 
"2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" 
       TCGA-CD-5799        TCGA-CD-5800        TCGA-CD-5801        TCGA-CD-5802 
"2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE"       "2P GAIN CNV"       "2P GAIN CNV" 
       TCGA-CD-5803        TCGA-CG-4300        TCGA-CG-4301        TCGA-CG-4304 
"2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" 
       TCGA-CG-4305        TCGA-CG-4306        TCGA-CG-4436        TCGA-CG-4437 
"2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" 
       TCGA-CG-4438        TCGA-CG-4440        TCGA-CG-4441        TCGA-CG-4443 
"2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" 
       TCGA-CG-4444        TCGA-CG-4449        TCGA-CG-4455        TCGA-CG-4460 
"2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE"       "2P GAIN CNV" 
       TCGA-CG-4462        TCGA-CG-4465        TCGA-CG-4466        TCGA-CG-4469 
"2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" 
       TCGA-CG-4472        TCGA-CG-4474        TCGA-CG-4477        TCGA-CG-5716 
      "2P GAIN CNV" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" 
       TCGA-CG-5717        TCGA-CG-5718        TCGA-CG-5719        TCGA-CG-5720 
"2P GAIN WILD-TYPE"       "2P GAIN CNV" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" 
       TCGA-CG-5721        TCGA-CG-5722        TCGA-CG-5723        TCGA-CG-5724 
"2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" 
       TCGA-CG-5725        TCGA-CG-5726        TCGA-CG-5727        TCGA-CG-5728 
"2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE"       "2P GAIN CNV" "2P GAIN WILD-TYPE" 
       TCGA-CG-5730        TCGA-CG-5732        TCGA-CG-5733        TCGA-CG-5734 
"2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" 
       TCGA-D7-5577        TCGA-D7-5578        TCGA-D7-5579        TCGA-D7-6518 
"2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" 
       TCGA-D7-6519        TCGA-D7-6520        TCGA-D7-6521        TCGA-D7-6522 
"2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" 
       TCGA-D7-6524        TCGA-D7-6525        TCGA-D7-6526        TCGA-D7-6527 
"2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" 
       TCGA-D7-6528        TCGA-D7-6815        TCGA-D7-6817        TCGA-D7-6818 
"2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" 
       TCGA-D7-6820        TCGA-D7-6822        TCGA-EQ-5647        TCGA-EQ-8122 
"2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" 
       TCGA-F1-6177        TCGA-F1-6874        TCGA-F1-6875        TCGA-FP-7735 
"2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" 
       TCGA-FP-7829        TCGA-FP-7916        TCGA-FP-7998        TCGA-FP-8099 
"2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" 
       TCGA-FP-8209        TCGA-FP-8210        TCGA-FP-8631        TCGA-HJ-7597 
"2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" 
       TCGA-IN-7806        TCGA-IN-7808        TCGA-IP-7968 
"2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" 
       TCGA-B7-5816        TCGA-B7-5818        TCGA-BR-6452        TCGA-BR-6455 
"2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" 
       TCGA-BR-6457        TCGA-BR-6458        TCGA-BR-6563        TCGA-BR-6564 
"2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" 
       TCGA-BR-6565        TCGA-BR-6566        TCGA-BR-6705        TCGA-BR-6706 
"2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" 
       TCGA-BR-6707        TCGA-BR-6709        TCGA-BR-6710        TCGA-BR-6801 
"2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" 
       TCGA-BR-6802        TCGA-BR-6803        TCGA-BR-6852        TCGA-BR-7196 
"2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" 
       TCGA-BR-7197        TCGA-BR-7703        TCGA-BR-7704        TCGA-BR-7707 
      "2P GAIN CNV" "2P GAIN WILD-TYPE"       "2P GAIN CNV" "2P GAIN WILD-TYPE" 
       TCGA-BR-7715        TCGA-BR-7716        TCGA-BR-7717        TCGA-BR-7722 
      "2P GAIN CNV" "2P GAIN WILD-TYPE"       "2P GAIN CNV" "2P GAIN WILD-TYPE" 
       TCGA-BR-7723        TCGA-BR-7851        TCGA-BR-7901        TCGA-BR-7957 
"2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" 
       TCGA-BR-7958        TCGA-BR-7959        TCGA-BR-8059        TCGA-BR-8060 
"2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" 
       TCGA-BR-8077        TCGA-BR-8078        TCGA-BR-8080        TCGA-BR-8081 
"2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" 
       TCGA-BR-8284        TCGA-BR-8285        TCGA-BR-8286        TCGA-BR-8289 
"2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" 
       TCGA-BR-8291        TCGA-BR-8295        TCGA-BR-8296        TCGA-BR-8297 
"2P GAIN WILD-TYPE"       "2P GAIN CNV" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" 
       TCGA-BR-8592        TCGA-BR-A4IU        TCGA-BR-A4IV        TCGA-BR-A4IY 
"2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE"       "2P GAIN CNV" 
       TCGA-BR-A4IZ        TCGA-BR-A4J1        TCGA-BR-A4J2        TCGA-BR-A4J4 
"2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" 
       TCGA-BR-A4J5        TCGA-BR-A4J6        TCGA-BR-A4J8        TCGA-BR-A4J9 
"2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" 
       TCGA-BR-A4PF        TCGA-BR-A4QI        TCGA-BR-A4QL        TCGA-CD-5798 
"2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" 
       TCGA-CD-5799        TCGA-CD-5800        TCGA-CD-5801        TCGA-CD-5802 
"2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE"       "2P GAIN CNV"       "2P GAIN CNV" 
       TCGA-CD-5803        TCGA-CG-4300        TCGA-CG-4301        TCGA-CG-4304 
"2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" 
       TCGA-CG-4305        TCGA-CG-4306        TCGA-CG-4436        TCGA-CG-4437 
"2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" 
       TCGA-CG-4438        TCGA-CG-4440        TCGA-CG-4441        TCGA-CG-4443 
"2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" 
       TCGA-CG-4444        TCGA-CG-4449        TCGA-CG-4455        TCGA-CG-4460 
"2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE"       "2P GAIN CNV" 
       TCGA-CG-4462        TCGA-CG-4465        TCGA-CG-4466        TCGA-CG-4469 
"2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" 
       TCGA-CG-4472        TCGA-CG-4474        TCGA-CG-4477        TCGA-CG-5716 
      "2P GAIN CNV" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" 
       TCGA-CG-5717        TCGA-CG-5718        TCGA-CG-5719        TCGA-CG-5720 
"2P GAIN WILD-TYPE"       "2P GAIN CNV" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" 
       TCGA-CG-5721        TCGA-CG-5722        TCGA-CG-5723        TCGA-CG-5724 
"2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" 
       TCGA-CG-5725        TCGA-CG-5726        TCGA-CG-5727        TCGA-CG-5728 
"2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE"       "2P GAIN CNV" "2P GAIN WILD-TYPE" 
       TCGA-CG-5730        TCGA-CG-5732        TCGA-CG-5733        TCGA-CG-5734 
"2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" 
       TCGA-D7-5577        TCGA-D7-5578        TCGA-D7-5579        TCGA-D7-6518 
"2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" 
       TCGA-D7-6519        TCGA-D7-6520        TCGA-D7-6521        TCGA-D7-6522 
"2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" 
       TCGA-D7-6524        TCGA-D7-6525        TCGA-D7-6526        TCGA-D7-6527 
"2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" 
       TCGA-D7-6528        TCGA-D7-6815        TCGA-D7-6817        TCGA-D7-6818 
"2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" 
       TCGA-D7-6820        TCGA-D7-6822        TCGA-EQ-5647        TCGA-EQ-8122 
"2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" 
       TCGA-F1-6177        TCGA-F1-6874        TCGA-F1-6875        TCGA-FP-7735 
"2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" 
       TCGA-FP-7829        TCGA-FP-7916        TCGA-FP-7998        TCGA-FP-8099 
"2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" 
       TCGA-FP-8209        TCGA-FP-8210        TCGA-FP-8631        TCGA-HJ-7597 
"2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" 
       TCGA-IN-7806        TCGA-IN-7808        TCGA-IP-7968 
"2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" 
[1] "hr=" "1.6"
D3V2, continuous
D3V3, binary
[1] "tbl2"
                   cls
clus                [,1] [,2]
  2P GAIN CNV          4    8
  2P GAIN WILD-TYPE   68  100
        clus
vv       2P GAIN CNV 2P GAIN WILD-TYPE
  FEMALE           4                68
  MALE             8               100
                   vv
clus                STOMACH  ADENOCARCINOMA  DIFFUSE TYPE
  2P GAIN CNV                                           0
  2P GAIN WILD-TYPE                                    10
                   vv
clus                STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  2P GAIN CNV                                                            2
  2P GAIN WILD-TYPE                                                     14
                   vv
clus                STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  2P GAIN CNV                                                                       0
  2P GAIN WILD-TYPE                                                                 8
                   vv
clus                STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE
  2P GAIN CNV                                                              0
  2P GAIN WILD-TYPE                                                        3
                   vv
clus                STOMACH ADENOCARCINOMA  SIGNET RING TYPE
  2P GAIN CNV                                              0
  2P GAIN WILD-TYPE                                        1
                   vv
clus                STOMACH ADENOCARCINOMA - DIFFUSE TYPE
  2P GAIN CNV                                           0
  2P GAIN WILD-TYPE                                    16
                   vv
clus                STOMACH ADENOCARCINOMA - NOT OTHERWISE SPECIFIED (NOS)
  2P GAIN CNV                                                            5
  2P GAIN WILD-TYPE                                                     68
                   vv
clus                STOMACH INTESTINAL ADENOCARCINOMA - MUCINOUS TYPE
  2P GAIN CNV                                                       0
  2P GAIN WILD-TYPE                                                 7
                   vv
clus                STOMACH INTESTINAL ADENOCARCINOMA - PAPILLARY TYPE
  2P GAIN CNV                                                        0
  2P GAIN WILD-TYPE                                                  3
                   vv
clus                STOMACH INTESTINAL ADENOCARCINOMA - TUBULAR TYPE
  2P GAIN CNV                                                      0
  2P GAIN WILD-TYPE                                               10
                   vv
clus                STOMACH INTESTINAL ADENOCARCINOMA - TYPE NOT OTHERWISE SPECIFIED (NOS)
  2P GAIN CNV                                                                            4
  2P GAIN WILD-TYPE                                                                     24
D3V4, multiclass
                   vv
clus                T1 T2 T3 T4
  2P GAIN CNV        0  1  6  3
  2P GAIN WILD-TYPE  6 51 50 15
D3V5, multiclass
    clus
vv   2P GAIN CNV 2P GAIN WILD-TYPE
  T1           0                 6
  T2           1                51
  T3           6                50
  T4           3                15
                   vv
clus                N0 N1 N2 N3
  2P GAIN CNV        5  5  0  0
  2P GAIN WILD-TYPE 39 44 23 15
D3V6, multiclass
    clus
vv   2P GAIN CNV 2P GAIN WILD-TYPE
  N0           5                39
  N1           5                44
  N2           0                23
  N3           0                15
                   vv
clus                 M0  M1  MX
  2P GAIN CNV         9   1   0
  2P GAIN WILD-TYPE 109  15   8
D3V7, multiclass
    clus
vv   2P GAIN CNV 2P GAIN WILD-TYPE
  M0           9               109
  M1           1                15
  MX           0                 8
                   vv
clus                 I II III IV
  2P GAIN CNV        0  6   1  3
  2P GAIN WILD-TYPE 24 31  38 23
D3V8, multiclass
     clus
vv    2P GAIN CNV 2P GAIN WILD-TYPE
  I             0                24
  II            6                31
  III           1                38
  IV            3                23
D3V9, binary
[1] "tbl2"
                   cls
clus                [,1] [,2]
  2P GAIN CNV          0   12
  2P GAIN WILD-TYPE    5  163
     clus
vv    2P GAIN CNV 2P GAIN WILD-TYPE
  NO            0                 5
  YES          12               163
                   vv
clus                 R0  R1  R2  RX
  2P GAIN CNV         9   0   1   0
  2P GAIN WILD-TYPE 116   7  11  25
D3V10, multiclass
    clus
vv   2P GAIN CNV 2P GAIN WILD-TYPE
  R0           9               116
  R1           0                 7
  R2           1                11
  RX           0                25
D3V11, continuous

Clustering(4) Variable = 2q gain
D4V1, survival
                   sevent
clus2                 0   1
  2Q GAIN CNV        11   2
  2Q GAIN WILD-TYPE 113  17
      2Q GAIN CNV 2Q GAIN WILD-TYPE 
               13               130 
      2Q GAIN CNV 2Q GAIN WILD-TYPE 
                2                17 
$`2Q GAIN CNV`
TCGA-BR-7197 TCGA-BR-7704 TCGA-BR-7715 TCGA-BR-7717 TCGA-BR-8295 TCGA-BR-A4IY 
        1.48         1.25         1.05         0.69         1.55         0.39 
TCGA-BR-A4J6 TCGA-CD-5801 TCGA-CG-4460 TCGA-CG-4472 TCGA-CG-5718 TCGA-CG-5727 
        0.13         0.49        21.99        12.00         1.02        31.04 
TCGA-F1-6875 
       72.23 

$`2Q GAIN WILD-TYPE`
TCGA-B7-5816 TCGA-B7-5818 TCGA-BR-6452 TCGA-BR-6455 TCGA-BR-6457 TCGA-BR-6458 
        5.62         0.10         0.95         1.41         1.35         1.35 
TCGA-BR-6563 TCGA-BR-6564 TCGA-BR-6565 TCGA-BR-6566 TCGA-BR-6705 TCGA-BR-6706 
        0.85         0.82         0.62         0.62         1.71         2.17 
TCGA-BR-6707 TCGA-BR-6709 TCGA-BR-6710 TCGA-BR-6801 TCGA-BR-6802 TCGA-BR-6803 
        0.99         1.22         0.66         1.12         0.76         0.66 
TCGA-BR-6852 TCGA-BR-7196 TCGA-BR-7703 TCGA-BR-7707 TCGA-BR-7716 TCGA-BR-7722 
        0.26         1.22         0.46         0.13         0.82         0.16 
TCGA-BR-7723 TCGA-BR-7851 TCGA-BR-7901 TCGA-BR-7957 TCGA-BR-7958 TCGA-BR-7959 
        4.54         0.99         0.95         0.69         0.16         1.08 
TCGA-BR-8059 TCGA-BR-8060 TCGA-BR-8077 TCGA-BR-8078 TCGA-BR-8080 TCGA-BR-8081 
        0.82         1.32         0.69         0.95         0.49         0.46 
TCGA-BR-8284 TCGA-BR-8285 TCGA-BR-8286 TCGA-BR-8289 TCGA-BR-8291 TCGA-BR-8296 
        0.72         0.26         0.43         0.26         1.18         1.48 
TCGA-BR-8297 TCGA-BR-8592 TCGA-BR-A4IU TCGA-BR-A4IV TCGA-BR-A4IZ TCGA-BR-A4J1 
        0.76         0.20         0.59         0.92         0.79         0.72 
TCGA-BR-A4J2 TCGA-BR-A4J4 TCGA-BR-A4J5 TCGA-BR-A4J8 TCGA-BR-A4J9 TCGA-BR-A4PF 
        0.79         0.53         0.43         0.23         0.10         0.72 
TCGA-BR-A4QI TCGA-BR-A4QL TCGA-CD-5798 TCGA-CD-5799 TCGA-CD-5800 TCGA-CD-5802 
        0.49         2.24         0.82         0.69         0.36         0.30 
TCGA-CD-5803 TCGA-CG-4300 TCGA-CG-4301 TCGA-CG-4304 TCGA-CG-4305 TCGA-CG-4306 
        0.07        20.02         3.02        27.02        15.95         1.02 
TCGA-CG-4436 TCGA-CG-4437 TCGA-CG-4438 TCGA-CG-4440 TCGA-CG-4441 TCGA-CG-4443 
       52.96         8.05        54.05         4.01        14.01        29.98 
TCGA-CG-4444 TCGA-CG-4449 TCGA-CG-4455 TCGA-CG-4462 TCGA-CG-4465 TCGA-CG-4466 
       47.05        19.07        12.03         1.02         8.98        18.94 
TCGA-CG-4469 TCGA-CG-4474 TCGA-CG-4477 TCGA-CG-5716 TCGA-CG-5717 TCGA-CG-5719 
        7.07         1.02         1.02         1.02         6.94         1.02 
TCGA-CG-5720 TCGA-CG-5721 TCGA-CG-5722 TCGA-CG-5723 TCGA-CG-5724 TCGA-CG-5725 
        0.99         5.98         0.95        70.06        12.03        15.02 
TCGA-CG-5726 TCGA-CG-5728 TCGA-CG-5730 TCGA-CG-5732 TCGA-CG-5733 TCGA-CG-5734 
       28.96        65.10         4.01        55.04        21.07         7.99 
TCGA-D7-5577 TCGA-D7-5578 TCGA-D7-5579 TCGA-D7-6518 TCGA-D7-6519 TCGA-D7-6520 
        8.65         3.58         4.54         9.80        15.65         9.63 
TCGA-D7-6521 TCGA-D7-6522 TCGA-D7-6524 TCGA-D7-6525 TCGA-D7-6526 TCGA-D7-6527 
        8.19         6.90         0.69         5.95         6.61         4.14 
TCGA-D7-6528 TCGA-D7-6815 TCGA-D7-6817 TCGA-D7-6818 TCGA-D7-6820 TCGA-D7-6822 
        1.68         3.65         4.70         4.04         2.93         4.27 
TCGA-EQ-5647 TCGA-EQ-8122 TCGA-F1-6177 TCGA-F1-6874 TCGA-FP-7735 TCGA-FP-7829 
        0.62         7.79         6.54         2.01         0.39         0.20 
TCGA-FP-7916 TCGA-FP-7998 TCGA-FP-8099 TCGA-FP-8209 TCGA-FP-8210 TCGA-FP-8631 
        3.02         3.58         1.02        59.05         5.03         0.56 
TCGA-HJ-7597 TCGA-IN-7806 TCGA-IN-7808 TCGA-IP-7968 
       26.43         6.87         3.55         2.53 

      2Q GAIN CNV 2Q GAIN WILD-TYPE 
             0.13              0.07 
      2Q GAIN CNV 2Q GAIN WILD-TYPE 
            72.23             70.06 
      2Q GAIN CNV 2Q GAIN WILD-TYPE 
             1.25              1.27 
[1] "0.1 - 72.2 (1.2)" "0.1 - 70.1 (1.3)"
       TCGA-B7-5816        TCGA-B7-5818        TCGA-BR-6452        TCGA-BR-6455 
"2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" 
       TCGA-BR-6457        TCGA-BR-6458        TCGA-BR-6563        TCGA-BR-6564 
"2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" 
       TCGA-BR-6565        TCGA-BR-6566        TCGA-BR-6705        TCGA-BR-6706 
"2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" 
       TCGA-BR-6707        TCGA-BR-6709        TCGA-BR-6710        TCGA-BR-6801 
"2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" 
       TCGA-BR-6802        TCGA-BR-6803        TCGA-BR-6852        TCGA-BR-7196 
"2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" 
       TCGA-BR-7197        TCGA-BR-7703        TCGA-BR-7704        TCGA-BR-7707 
      "2Q GAIN CNV" "2Q GAIN WILD-TYPE"       "2Q GAIN CNV" "2Q GAIN WILD-TYPE" 
       TCGA-BR-7715        TCGA-BR-7716        TCGA-BR-7717        TCGA-BR-7722 
      "2Q GAIN CNV" "2Q GAIN WILD-TYPE"       "2Q GAIN CNV" "2Q GAIN WILD-TYPE" 
       TCGA-BR-7723        TCGA-BR-7851        TCGA-BR-7901        TCGA-BR-7957 
"2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" 
       TCGA-BR-7958        TCGA-BR-7959        TCGA-BR-8059        TCGA-BR-8060 
"2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" 
       TCGA-BR-8077        TCGA-BR-8078        TCGA-BR-8080        TCGA-BR-8081 
"2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" 
       TCGA-BR-8284        TCGA-BR-8285        TCGA-BR-8286        TCGA-BR-8289 
"2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" 
       TCGA-BR-8291        TCGA-BR-8295        TCGA-BR-8296        TCGA-BR-8297 
"2Q GAIN WILD-TYPE"       "2Q GAIN CNV" "2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" 
       TCGA-BR-8592        TCGA-BR-A4IU        TCGA-BR-A4IV        TCGA-BR-A4IY 
"2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE"       "2Q GAIN CNV" 
       TCGA-BR-A4IZ        TCGA-BR-A4J1        TCGA-BR-A4J2        TCGA-BR-A4J4 
"2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" 
       TCGA-BR-A4J5        TCGA-BR-A4J6        TCGA-BR-A4J8        TCGA-BR-A4J9 
"2Q GAIN WILD-TYPE"       "2Q GAIN CNV" "2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" 
       TCGA-BR-A4PF        TCGA-BR-A4QI        TCGA-BR-A4QL        TCGA-CD-5798 
"2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" 
       TCGA-CD-5799        TCGA-CD-5800        TCGA-CD-5801        TCGA-CD-5802 
"2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE"       "2Q GAIN CNV" "2Q GAIN WILD-TYPE" 
       TCGA-CD-5803        TCGA-CG-4300        TCGA-CG-4301        TCGA-CG-4304 
"2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" 
       TCGA-CG-4305        TCGA-CG-4306        TCGA-CG-4436        TCGA-CG-4437 
"2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" 
       TCGA-CG-4438        TCGA-CG-4440        TCGA-CG-4441        TCGA-CG-4443 
"2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" 
       TCGA-CG-4444        TCGA-CG-4449        TCGA-CG-4455        TCGA-CG-4460 
"2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE"       "2Q GAIN CNV" 
       TCGA-CG-4462        TCGA-CG-4465        TCGA-CG-4466        TCGA-CG-4469 
"2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" 
       TCGA-CG-4472        TCGA-CG-4474        TCGA-CG-4477        TCGA-CG-5716 
      "2Q GAIN CNV" "2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" 
       TCGA-CG-5717        TCGA-CG-5718        TCGA-CG-5719        TCGA-CG-5720 
"2Q GAIN WILD-TYPE"       "2Q GAIN CNV" "2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" 
       TCGA-CG-5721        TCGA-CG-5722        TCGA-CG-5723        TCGA-CG-5724 
"2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" 
       TCGA-CG-5725        TCGA-CG-5726        TCGA-CG-5727        TCGA-CG-5728 
"2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE"       "2Q GAIN CNV" "2Q GAIN WILD-TYPE" 
       TCGA-CG-5730        TCGA-CG-5732        TCGA-CG-5733        TCGA-CG-5734 
"2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" 
       TCGA-D7-5577        TCGA-D7-5578        TCGA-D7-5579        TCGA-D7-6518 
"2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" 
       TCGA-D7-6519        TCGA-D7-6520        TCGA-D7-6521        TCGA-D7-6522 
"2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" 
       TCGA-D7-6524        TCGA-D7-6525        TCGA-D7-6526        TCGA-D7-6527 
"2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" 
       TCGA-D7-6528        TCGA-D7-6815        TCGA-D7-6817        TCGA-D7-6818 
"2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" 
       TCGA-D7-6820        TCGA-D7-6822        TCGA-EQ-5647        TCGA-EQ-8122 
"2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" 
       TCGA-F1-6177        TCGA-F1-6874        TCGA-F1-6875        TCGA-FP-7735 
"2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE"       "2Q GAIN CNV" "2Q GAIN WILD-TYPE" 
       TCGA-FP-7829        TCGA-FP-7916        TCGA-FP-7998        TCGA-FP-8099 
"2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" 
       TCGA-FP-8209        TCGA-FP-8210        TCGA-FP-8631        TCGA-HJ-7597 
"2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" 
       TCGA-IN-7806        TCGA-IN-7808        TCGA-IP-7968 
"2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" 
       TCGA-B7-5816        TCGA-B7-5818        TCGA-BR-6452        TCGA-BR-6455 
"2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" 
       TCGA-BR-6457        TCGA-BR-6458        TCGA-BR-6563        TCGA-BR-6564 
"2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" 
       TCGA-BR-6565        TCGA-BR-6566        TCGA-BR-6705        TCGA-BR-6706 
"2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" 
       TCGA-BR-6707        TCGA-BR-6709        TCGA-BR-6710        TCGA-BR-6801 
"2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" 
       TCGA-BR-6802        TCGA-BR-6803        TCGA-BR-6852        TCGA-BR-7196 
"2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" 
       TCGA-BR-7197        TCGA-BR-7703        TCGA-BR-7704        TCGA-BR-7707 
      "2Q GAIN CNV" "2Q GAIN WILD-TYPE"       "2Q GAIN CNV" "2Q GAIN WILD-TYPE" 
       TCGA-BR-7715        TCGA-BR-7716        TCGA-BR-7717        TCGA-BR-7722 
      "2Q GAIN CNV" "2Q GAIN WILD-TYPE"       "2Q GAIN CNV" "2Q GAIN WILD-TYPE" 
       TCGA-BR-7723        TCGA-BR-7851        TCGA-BR-7901        TCGA-BR-7957 
"2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" 
       TCGA-BR-7958        TCGA-BR-7959        TCGA-BR-8059        TCGA-BR-8060 
"2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" 
       TCGA-BR-8077        TCGA-BR-8078        TCGA-BR-8080        TCGA-BR-8081 
"2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" 
       TCGA-BR-8284        TCGA-BR-8285        TCGA-BR-8286        TCGA-BR-8289 
"2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" 
       TCGA-BR-8291        TCGA-BR-8295        TCGA-BR-8296        TCGA-BR-8297 
"2Q GAIN WILD-TYPE"       "2Q GAIN CNV" "2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" 
       TCGA-BR-8592        TCGA-BR-A4IU        TCGA-BR-A4IV        TCGA-BR-A4IY 
"2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE"       "2Q GAIN CNV" 
       TCGA-BR-A4IZ        TCGA-BR-A4J1        TCGA-BR-A4J2        TCGA-BR-A4J4 
"2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" 
       TCGA-BR-A4J5        TCGA-BR-A4J6        TCGA-BR-A4J8        TCGA-BR-A4J9 
"2Q GAIN WILD-TYPE"       "2Q GAIN CNV" "2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" 
       TCGA-BR-A4PF        TCGA-BR-A4QI        TCGA-BR-A4QL        TCGA-CD-5798 
"2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" 
       TCGA-CD-5799        TCGA-CD-5800        TCGA-CD-5801        TCGA-CD-5802 
"2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE"       "2Q GAIN CNV" "2Q GAIN WILD-TYPE" 
       TCGA-CD-5803        TCGA-CG-4300        TCGA-CG-4301        TCGA-CG-4304 
"2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" 
       TCGA-CG-4305        TCGA-CG-4306        TCGA-CG-4436        TCGA-CG-4437 
"2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" 
       TCGA-CG-4438        TCGA-CG-4440        TCGA-CG-4441        TCGA-CG-4443 
"2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" 
       TCGA-CG-4444        TCGA-CG-4449        TCGA-CG-4455        TCGA-CG-4460 
"2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE"       "2Q GAIN CNV" 
       TCGA-CG-4462        TCGA-CG-4465        TCGA-CG-4466        TCGA-CG-4469 
"2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" 
       TCGA-CG-4472        TCGA-CG-4474        TCGA-CG-4477        TCGA-CG-5716 
      "2Q GAIN CNV" "2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" 
       TCGA-CG-5717        TCGA-CG-5718        TCGA-CG-5719        TCGA-CG-5720 
"2Q GAIN WILD-TYPE"       "2Q GAIN CNV" "2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" 
       TCGA-CG-5721        TCGA-CG-5722        TCGA-CG-5723        TCGA-CG-5724 
"2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" 
       TCGA-CG-5725        TCGA-CG-5726        TCGA-CG-5727        TCGA-CG-5728 
"2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE"       "2Q GAIN CNV" "2Q GAIN WILD-TYPE" 
       TCGA-CG-5730        TCGA-CG-5732        TCGA-CG-5733        TCGA-CG-5734 
"2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" 
       TCGA-D7-5577        TCGA-D7-5578        TCGA-D7-5579        TCGA-D7-6518 
"2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" 
       TCGA-D7-6519        TCGA-D7-6520        TCGA-D7-6521        TCGA-D7-6522 
"2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" 
       TCGA-D7-6524        TCGA-D7-6525        TCGA-D7-6526        TCGA-D7-6527 
"2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" 
       TCGA-D7-6528        TCGA-D7-6815        TCGA-D7-6817        TCGA-D7-6818 
"2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" 
       TCGA-D7-6820        TCGA-D7-6822        TCGA-EQ-5647        TCGA-EQ-8122 
"2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" 
       TCGA-F1-6177        TCGA-F1-6874        TCGA-F1-6875        TCGA-FP-7735 
"2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE"       "2Q GAIN CNV" "2Q GAIN WILD-TYPE" 
       TCGA-FP-7829        TCGA-FP-7916        TCGA-FP-7998        TCGA-FP-8099 
"2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" 
       TCGA-FP-8209        TCGA-FP-8210        TCGA-FP-8631        TCGA-HJ-7597 
"2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" 
       TCGA-IN-7806        TCGA-IN-7808        TCGA-IP-7968 
"2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" 
       TCGA-B7-5816        TCGA-B7-5818        TCGA-BR-6452        TCGA-BR-6455 
"2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" 
       TCGA-BR-6457        TCGA-BR-6458        TCGA-BR-6563        TCGA-BR-6564 
"2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" 
       TCGA-BR-6565        TCGA-BR-6566        TCGA-BR-6705        TCGA-BR-6706 
"2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" 
       TCGA-BR-6707        TCGA-BR-6709        TCGA-BR-6710        TCGA-BR-6801 
"2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" 
       TCGA-BR-6802        TCGA-BR-6803        TCGA-BR-6852        TCGA-BR-7196 
"2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" 
       TCGA-BR-7197        TCGA-BR-7703        TCGA-BR-7704        TCGA-BR-7707 
      "2Q GAIN CNV" "2Q GAIN WILD-TYPE"       "2Q GAIN CNV" "2Q GAIN WILD-TYPE" 
       TCGA-BR-7715        TCGA-BR-7716        TCGA-BR-7717        TCGA-BR-7722 
      "2Q GAIN CNV" "2Q GAIN WILD-TYPE"       "2Q GAIN CNV" "2Q GAIN WILD-TYPE" 
       TCGA-BR-7723        TCGA-BR-7851        TCGA-BR-7901        TCGA-BR-7957 
"2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" 
       TCGA-BR-7958        TCGA-BR-7959        TCGA-BR-8059        TCGA-BR-8060 
"2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" 
       TCGA-BR-8077        TCGA-BR-8078        TCGA-BR-8080        TCGA-BR-8081 
"2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" 
       TCGA-BR-8284        TCGA-BR-8285        TCGA-BR-8286        TCGA-BR-8289 
"2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" 
       TCGA-BR-8291        TCGA-BR-8295        TCGA-BR-8296        TCGA-BR-8297 
"2Q GAIN WILD-TYPE"       "2Q GAIN CNV" "2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" 
       TCGA-BR-8592        TCGA-BR-A4IU        TCGA-BR-A4IV        TCGA-BR-A4IY 
"2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE"       "2Q GAIN CNV" 
       TCGA-BR-A4IZ        TCGA-BR-A4J1        TCGA-BR-A4J2        TCGA-BR-A4J4 
"2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" 
       TCGA-BR-A4J5        TCGA-BR-A4J6        TCGA-BR-A4J8        TCGA-BR-A4J9 
"2Q GAIN WILD-TYPE"       "2Q GAIN CNV" "2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" 
       TCGA-BR-A4PF        TCGA-BR-A4QI        TCGA-BR-A4QL        TCGA-CD-5798 
"2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" 
       TCGA-CD-5799        TCGA-CD-5800        TCGA-CD-5801        TCGA-CD-5802 
"2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE"       "2Q GAIN CNV" "2Q GAIN WILD-TYPE" 
       TCGA-CD-5803        TCGA-CG-4300        TCGA-CG-4301        TCGA-CG-4304 
"2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" 
       TCGA-CG-4305        TCGA-CG-4306        TCGA-CG-4436        TCGA-CG-4437 
"2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" 
       TCGA-CG-4438        TCGA-CG-4440        TCGA-CG-4441        TCGA-CG-4443 
"2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" 
       TCGA-CG-4444        TCGA-CG-4449        TCGA-CG-4455        TCGA-CG-4460 
"2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE"       "2Q GAIN CNV" 
       TCGA-CG-4462        TCGA-CG-4465        TCGA-CG-4466        TCGA-CG-4469 
"2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" 
       TCGA-CG-4472        TCGA-CG-4474        TCGA-CG-4477        TCGA-CG-5716 
      "2Q GAIN CNV" "2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" 
       TCGA-CG-5717        TCGA-CG-5718        TCGA-CG-5719        TCGA-CG-5720 
"2Q GAIN WILD-TYPE"       "2Q GAIN CNV" "2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" 
       TCGA-CG-5721        TCGA-CG-5722        TCGA-CG-5723        TCGA-CG-5724 
"2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" 
       TCGA-CG-5725        TCGA-CG-5726        TCGA-CG-5727        TCGA-CG-5728 
"2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE"       "2Q GAIN CNV" "2Q GAIN WILD-TYPE" 
       TCGA-CG-5730        TCGA-CG-5732        TCGA-CG-5733        TCGA-CG-5734 
"2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" 
       TCGA-D7-5577        TCGA-D7-5578        TCGA-D7-5579        TCGA-D7-6518 
"2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" 
       TCGA-D7-6519        TCGA-D7-6520        TCGA-D7-6521        TCGA-D7-6522 
"2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" 
       TCGA-D7-6524        TCGA-D7-6525        TCGA-D7-6526        TCGA-D7-6527 
"2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" 
       TCGA-D7-6528        TCGA-D7-6815        TCGA-D7-6817        TCGA-D7-6818 
"2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" 
       TCGA-D7-6820        TCGA-D7-6822        TCGA-EQ-5647        TCGA-EQ-8122 
"2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" 
       TCGA-F1-6177        TCGA-F1-6874        TCGA-F1-6875        TCGA-FP-7735 
"2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE"       "2Q GAIN CNV" "2Q GAIN WILD-TYPE" 
       TCGA-FP-7829        TCGA-FP-7916        TCGA-FP-7998        TCGA-FP-8099 
"2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" 
       TCGA-FP-8209        TCGA-FP-8210        TCGA-FP-8631        TCGA-HJ-7597 
"2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" 
       TCGA-IN-7806        TCGA-IN-7808        TCGA-IP-7968 
"2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" 
[1] "hr=" "2.7"
D4V2, continuous
D4V3, binary
[1] "tbl2"
                   cls
clus                [,1] [,2]
  2Q GAIN CNV          5    9
  2Q GAIN WILD-TYPE   67   99
        clus
vv       2Q GAIN CNV 2Q GAIN WILD-TYPE
  FEMALE           5                67
  MALE             9                99
                   vv
clus                STOMACH  ADENOCARCINOMA  DIFFUSE TYPE
  2Q GAIN CNV                                           0
  2Q GAIN WILD-TYPE                                    10
                   vv
clus                STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  2Q GAIN CNV                                                            3
  2Q GAIN WILD-TYPE                                                     13
                   vv
clus                STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  2Q GAIN CNV                                                                       0
  2Q GAIN WILD-TYPE                                                                 8
                   vv
clus                STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE
  2Q GAIN CNV                                                              0
  2Q GAIN WILD-TYPE                                                        3
                   vv
clus                STOMACH ADENOCARCINOMA  SIGNET RING TYPE
  2Q GAIN CNV                                              0
  2Q GAIN WILD-TYPE                                        1
                   vv
clus                STOMACH ADENOCARCINOMA - DIFFUSE TYPE
  2Q GAIN CNV                                           0
  2Q GAIN WILD-TYPE                                    16
                   vv
clus                STOMACH ADENOCARCINOMA - NOT OTHERWISE SPECIFIED (NOS)
  2Q GAIN CNV                                                            6
  2Q GAIN WILD-TYPE                                                     67
                   vv
clus                STOMACH INTESTINAL ADENOCARCINOMA - MUCINOUS TYPE
  2Q GAIN CNV                                                       0
  2Q GAIN WILD-TYPE                                                 7
                   vv
clus                STOMACH INTESTINAL ADENOCARCINOMA - PAPILLARY TYPE
  2Q GAIN CNV                                                        0
  2Q GAIN WILD-TYPE                                                  3
                   vv
clus                STOMACH INTESTINAL ADENOCARCINOMA - TUBULAR TYPE
  2Q GAIN CNV                                                      0
  2Q GAIN WILD-TYPE                                               10
                   vv
clus                STOMACH INTESTINAL ADENOCARCINOMA - TYPE NOT OTHERWISE SPECIFIED (NOS)
  2Q GAIN CNV                                                                            4
  2Q GAIN WILD-TYPE                                                                     24
D4V4, multiclass
                   vv
clus                T1 T2 T3 T4
  2Q GAIN CNV        0  2  6  3
  2Q GAIN WILD-TYPE  6 50 50 15
D4V5, multiclass
    clus
vv   2Q GAIN CNV 2Q GAIN WILD-TYPE
  T1           0                 6
  T2           2                50
  T3           6                50
  T4           3                15
                   vv
clus                N0 N1 N2 N3
  2Q GAIN CNV        5  5  0  0
  2Q GAIN WILD-TYPE 39 44 23 15
D4V6, multiclass
    clus
vv   2Q GAIN CNV 2Q GAIN WILD-TYPE
  N0           5                39
  N1           5                44
  N2           0                23
  N3           0                15
                   vv
clus                 M0  M1  MX
  2Q GAIN CNV         9   1   1
  2Q GAIN WILD-TYPE 109  15   7
D4V7, multiclass
    clus
vv   2Q GAIN CNV 2Q GAIN WILD-TYPE
  M0           9               109
  M1           1                15
  MX           1                 7
                   vv
clus                 I II III IV
  2Q GAIN CNV        1  5   1  3
  2Q GAIN WILD-TYPE 23 32  38 23
D4V8, multiclass
     clus
vv    2Q GAIN CNV 2Q GAIN WILD-TYPE
  I             1                23
  II            5                32
  III           1                38
  IV            3                23
D4V9, binary
[1] "tbl2"
                   cls
clus                [,1] [,2]
  2Q GAIN CNV          0   14
  2Q GAIN WILD-TYPE    5  161
     clus
vv    2Q GAIN CNV 2Q GAIN WILD-TYPE
  NO            0                 5
  YES          14               161
                   vv
clus                 R0  R1  R2  RX
  2Q GAIN CNV        11   0   1   1
  2Q GAIN WILD-TYPE 114   7  11  24
D4V10, multiclass
    clus
vv   2Q GAIN CNV 2Q GAIN WILD-TYPE
  R0          11               114
  R1           0                 7
  R2           1                11
  RX           1                24
D4V11, continuous

Clustering(5) Variable = 3p gain
D5V1, survival
                   sevent
clus2                 0   1
  3P GAIN CNV         1   0
  3P GAIN WILD-TYPE 123  19
      3P GAIN CNV 3P GAIN WILD-TYPE 
                1               142 
      3P GAIN CNV 3P GAIN WILD-TYPE 
                0                19 
$`3P GAIN CNV`
TCGA-BR-7722 
        0.16 

$`3P GAIN WILD-TYPE`
TCGA-B7-5816 TCGA-B7-5818 TCGA-BR-6452 TCGA-BR-6455 TCGA-BR-6457 TCGA-BR-6458 
        5.62         0.10         0.95         1.41         1.35         1.35 
TCGA-BR-6563 TCGA-BR-6564 TCGA-BR-6565 TCGA-BR-6566 TCGA-BR-6705 TCGA-BR-6706 
        0.85         0.82         0.62         0.62         1.71         2.17 
TCGA-BR-6707 TCGA-BR-6709 TCGA-BR-6710 TCGA-BR-6801 TCGA-BR-6802 TCGA-BR-6803 
        0.99         1.22         0.66         1.12         0.76         0.66 
TCGA-BR-6852 TCGA-BR-7196 TCGA-BR-7197 TCGA-BR-7703 TCGA-BR-7704 TCGA-BR-7707 
        0.26         1.22         1.48         0.46         1.25         0.13 
TCGA-BR-7715 TCGA-BR-7716 TCGA-BR-7717 TCGA-BR-7723 TCGA-BR-7851 TCGA-BR-7901 
        1.05         0.82         0.69         4.54         0.99         0.95 
TCGA-BR-7957 TCGA-BR-7958 TCGA-BR-7959 TCGA-BR-8059 TCGA-BR-8060 TCGA-BR-8077 
        0.69         0.16         1.08         0.82         1.32         0.69 
TCGA-BR-8078 TCGA-BR-8080 TCGA-BR-8081 TCGA-BR-8284 TCGA-BR-8285 TCGA-BR-8286 
        0.95         0.49         0.46         0.72         0.26         0.43 
TCGA-BR-8289 TCGA-BR-8291 TCGA-BR-8295 TCGA-BR-8296 TCGA-BR-8297 TCGA-BR-8592 
        0.26         1.18         1.55         1.48         0.76         0.20 
TCGA-BR-A4IU TCGA-BR-A4IV TCGA-BR-A4IY TCGA-BR-A4IZ TCGA-BR-A4J1 TCGA-BR-A4J2 
        0.59         0.92         0.39         0.79         0.72         0.79 
TCGA-BR-A4J4 TCGA-BR-A4J5 TCGA-BR-A4J6 TCGA-BR-A4J8 TCGA-BR-A4J9 TCGA-BR-A4PF 
        0.53         0.43         0.13         0.23         0.10         0.72 
TCGA-BR-A4QI TCGA-BR-A4QL TCGA-CD-5798 TCGA-CD-5799 TCGA-CD-5800 TCGA-CD-5801 
        0.49         2.24         0.82         0.69         0.36         0.49 
TCGA-CD-5802 TCGA-CD-5803 TCGA-CG-4300 TCGA-CG-4301 TCGA-CG-4304 TCGA-CG-4305 
        0.30         0.07        20.02         3.02        27.02        15.95 
TCGA-CG-4306 TCGA-CG-4436 TCGA-CG-4437 TCGA-CG-4438 TCGA-CG-4440 TCGA-CG-4441 
        1.02        52.96         8.05        54.05         4.01        14.01 
TCGA-CG-4443 TCGA-CG-4444 TCGA-CG-4449 TCGA-CG-4455 TCGA-CG-4460 TCGA-CG-4462 
       29.98        47.05        19.07        12.03        21.99         1.02 
TCGA-CG-4465 TCGA-CG-4466 TCGA-CG-4469 TCGA-CG-4472 TCGA-CG-4474 TCGA-CG-4477 
        8.98        18.94         7.07        12.00         1.02         1.02 
TCGA-CG-5716 TCGA-CG-5717 TCGA-CG-5718 TCGA-CG-5719 TCGA-CG-5720 TCGA-CG-5721 
        1.02         6.94         1.02         1.02         0.99         5.98 
TCGA-CG-5722 TCGA-CG-5723 TCGA-CG-5724 TCGA-CG-5725 TCGA-CG-5726 TCGA-CG-5727 
        0.95        70.06        12.03        15.02        28.96        31.04 
TCGA-CG-5728 TCGA-CG-5730 TCGA-CG-5732 TCGA-CG-5733 TCGA-CG-5734 TCGA-D7-5577 
       65.10         4.01        55.04        21.07         7.99         8.65 
TCGA-D7-5578 TCGA-D7-5579 TCGA-D7-6518 TCGA-D7-6519 TCGA-D7-6520 TCGA-D7-6521 
        3.58         4.54         9.80        15.65         9.63         8.19 
TCGA-D7-6522 TCGA-D7-6524 TCGA-D7-6525 TCGA-D7-6526 TCGA-D7-6527 TCGA-D7-6528 
        6.90         0.69         5.95         6.61         4.14         1.68 
TCGA-D7-6815 TCGA-D7-6817 TCGA-D7-6818 TCGA-D7-6820 TCGA-D7-6822 TCGA-EQ-5647 
        3.65         4.70         4.04         2.93         4.27         0.62 
TCGA-EQ-8122 TCGA-F1-6177 TCGA-F1-6874 TCGA-F1-6875 TCGA-FP-7735 TCGA-FP-7829 
        7.79         6.54         2.01        72.23         0.39         0.20 
TCGA-FP-7916 TCGA-FP-7998 TCGA-FP-8099 TCGA-FP-8209 TCGA-FP-8210 TCGA-FP-8631 
        3.02         3.58         1.02        59.05         5.03         0.56 
TCGA-HJ-7597 TCGA-IN-7806 TCGA-IN-7808 TCGA-IP-7968 
       26.43         6.87         3.55         2.53 

      3P GAIN CNV 3P GAIN WILD-TYPE 
             0.16              0.07 
      3P GAIN CNV 3P GAIN WILD-TYPE 
             0.16             72.23 
      3P GAIN CNV 3P GAIN WILD-TYPE 
            0.160             1.285 
[1] "0.2 - 0.2 (0.2)"  "0.1 - 72.2 (1.3)"
       TCGA-B7-5816        TCGA-B7-5818        TCGA-BR-6452        TCGA-BR-6455 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-BR-6457        TCGA-BR-6458        TCGA-BR-6563        TCGA-BR-6564 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-BR-6565        TCGA-BR-6566        TCGA-BR-6705        TCGA-BR-6706 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-BR-6707        TCGA-BR-6709        TCGA-BR-6710        TCGA-BR-6801 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-BR-6802        TCGA-BR-6803        TCGA-BR-6852        TCGA-BR-7196 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-BR-7197        TCGA-BR-7703        TCGA-BR-7704        TCGA-BR-7707 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-BR-7715        TCGA-BR-7716        TCGA-BR-7717        TCGA-BR-7722 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE"       "3P GAIN CNV" 
       TCGA-BR-7723        TCGA-BR-7851        TCGA-BR-7901        TCGA-BR-7957 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-BR-7958        TCGA-BR-7959        TCGA-BR-8059        TCGA-BR-8060 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-BR-8077        TCGA-BR-8078        TCGA-BR-8080        TCGA-BR-8081 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-BR-8284        TCGA-BR-8285        TCGA-BR-8286        TCGA-BR-8289 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-BR-8291        TCGA-BR-8295        TCGA-BR-8296        TCGA-BR-8297 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-BR-8592        TCGA-BR-A4IU        TCGA-BR-A4IV        TCGA-BR-A4IY 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-BR-A4IZ        TCGA-BR-A4J1        TCGA-BR-A4J2        TCGA-BR-A4J4 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-BR-A4J5        TCGA-BR-A4J6        TCGA-BR-A4J8        TCGA-BR-A4J9 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-BR-A4PF        TCGA-BR-A4QI        TCGA-BR-A4QL        TCGA-CD-5798 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-CD-5799        TCGA-CD-5800        TCGA-CD-5801        TCGA-CD-5802 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-CD-5803        TCGA-CG-4300        TCGA-CG-4301        TCGA-CG-4304 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-CG-4305        TCGA-CG-4306        TCGA-CG-4436        TCGA-CG-4437 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-CG-4438        TCGA-CG-4440        TCGA-CG-4441        TCGA-CG-4443 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-CG-4444        TCGA-CG-4449        TCGA-CG-4455        TCGA-CG-4460 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-CG-4462        TCGA-CG-4465        TCGA-CG-4466        TCGA-CG-4469 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-CG-4472        TCGA-CG-4474        TCGA-CG-4477        TCGA-CG-5716 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-CG-5717        TCGA-CG-5718        TCGA-CG-5719        TCGA-CG-5720 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-CG-5721        TCGA-CG-5722        TCGA-CG-5723        TCGA-CG-5724 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-CG-5725        TCGA-CG-5726        TCGA-CG-5727        TCGA-CG-5728 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-CG-5730        TCGA-CG-5732        TCGA-CG-5733        TCGA-CG-5734 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-D7-5577        TCGA-D7-5578        TCGA-D7-5579        TCGA-D7-6518 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-D7-6519        TCGA-D7-6520        TCGA-D7-6521        TCGA-D7-6522 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-D7-6524        TCGA-D7-6525        TCGA-D7-6526        TCGA-D7-6527 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-D7-6528        TCGA-D7-6815        TCGA-D7-6817        TCGA-D7-6818 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-D7-6820        TCGA-D7-6822        TCGA-EQ-5647        TCGA-EQ-8122 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-F1-6177        TCGA-F1-6874        TCGA-F1-6875        TCGA-FP-7735 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-FP-7829        TCGA-FP-7916        TCGA-FP-7998        TCGA-FP-8099 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-FP-8209        TCGA-FP-8210        TCGA-FP-8631        TCGA-HJ-7597 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-IN-7806        TCGA-IN-7808        TCGA-IP-7968 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-B7-5816        TCGA-B7-5818        TCGA-BR-6452        TCGA-BR-6455 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-BR-6457        TCGA-BR-6458        TCGA-BR-6563        TCGA-BR-6564 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-BR-6565        TCGA-BR-6566        TCGA-BR-6705        TCGA-BR-6706 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-BR-6707        TCGA-BR-6709        TCGA-BR-6710        TCGA-BR-6801 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-BR-6802        TCGA-BR-6803        TCGA-BR-6852        TCGA-BR-7196 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-BR-7197        TCGA-BR-7703        TCGA-BR-7704        TCGA-BR-7707 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-BR-7715        TCGA-BR-7716        TCGA-BR-7717        TCGA-BR-7722 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE"       "3P GAIN CNV" 
       TCGA-BR-7723        TCGA-BR-7851        TCGA-BR-7901        TCGA-BR-7957 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-BR-7958        TCGA-BR-7959        TCGA-BR-8059        TCGA-BR-8060 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-BR-8077        TCGA-BR-8078        TCGA-BR-8080        TCGA-BR-8081 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-BR-8284        TCGA-BR-8285        TCGA-BR-8286        TCGA-BR-8289 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-BR-8291        TCGA-BR-8295        TCGA-BR-8296        TCGA-BR-8297 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-BR-8592        TCGA-BR-A4IU        TCGA-BR-A4IV        TCGA-BR-A4IY 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-BR-A4IZ        TCGA-BR-A4J1        TCGA-BR-A4J2        TCGA-BR-A4J4 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-BR-A4J5        TCGA-BR-A4J6        TCGA-BR-A4J8        TCGA-BR-A4J9 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-BR-A4PF        TCGA-BR-A4QI        TCGA-BR-A4QL        TCGA-CD-5798 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-CD-5799        TCGA-CD-5800        TCGA-CD-5801        TCGA-CD-5802 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-CD-5803        TCGA-CG-4300        TCGA-CG-4301        TCGA-CG-4304 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-CG-4305        TCGA-CG-4306        TCGA-CG-4436        TCGA-CG-4437 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-CG-4438        TCGA-CG-4440        TCGA-CG-4441        TCGA-CG-4443 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-CG-4444        TCGA-CG-4449        TCGA-CG-4455        TCGA-CG-4460 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-CG-4462        TCGA-CG-4465        TCGA-CG-4466        TCGA-CG-4469 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-CG-4472        TCGA-CG-4474        TCGA-CG-4477        TCGA-CG-5716 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-CG-5717        TCGA-CG-5718        TCGA-CG-5719        TCGA-CG-5720 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-CG-5721        TCGA-CG-5722        TCGA-CG-5723        TCGA-CG-5724 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-CG-5725        TCGA-CG-5726        TCGA-CG-5727        TCGA-CG-5728 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-CG-5730        TCGA-CG-5732        TCGA-CG-5733        TCGA-CG-5734 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-D7-5577        TCGA-D7-5578        TCGA-D7-5579        TCGA-D7-6518 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-D7-6519        TCGA-D7-6520        TCGA-D7-6521        TCGA-D7-6522 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-D7-6524        TCGA-D7-6525        TCGA-D7-6526        TCGA-D7-6527 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-D7-6528        TCGA-D7-6815        TCGA-D7-6817        TCGA-D7-6818 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-D7-6820        TCGA-D7-6822        TCGA-EQ-5647        TCGA-EQ-8122 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-F1-6177        TCGA-F1-6874        TCGA-F1-6875        TCGA-FP-7735 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-FP-7829        TCGA-FP-7916        TCGA-FP-7998        TCGA-FP-8099 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-FP-8209        TCGA-FP-8210        TCGA-FP-8631        TCGA-HJ-7597 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-IN-7806        TCGA-IN-7808        TCGA-IP-7968 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-B7-5816        TCGA-B7-5818        TCGA-BR-6452        TCGA-BR-6455 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-BR-6457        TCGA-BR-6458        TCGA-BR-6563        TCGA-BR-6564 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-BR-6565        TCGA-BR-6566        TCGA-BR-6705        TCGA-BR-6706 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-BR-6707        TCGA-BR-6709        TCGA-BR-6710        TCGA-BR-6801 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-BR-6802        TCGA-BR-6803        TCGA-BR-6852        TCGA-BR-7196 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-BR-7197        TCGA-BR-7703        TCGA-BR-7704        TCGA-BR-7707 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-BR-7715        TCGA-BR-7716        TCGA-BR-7717        TCGA-BR-7722 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE"       "3P GAIN CNV" 
       TCGA-BR-7723        TCGA-BR-7851        TCGA-BR-7901        TCGA-BR-7957 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-BR-7958        TCGA-BR-7959        TCGA-BR-8059        TCGA-BR-8060 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-BR-8077        TCGA-BR-8078        TCGA-BR-8080        TCGA-BR-8081 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-BR-8284        TCGA-BR-8285        TCGA-BR-8286        TCGA-BR-8289 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-BR-8291        TCGA-BR-8295        TCGA-BR-8296        TCGA-BR-8297 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-BR-8592        TCGA-BR-A4IU        TCGA-BR-A4IV        TCGA-BR-A4IY 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-BR-A4IZ        TCGA-BR-A4J1        TCGA-BR-A4J2        TCGA-BR-A4J4 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-BR-A4J5        TCGA-BR-A4J6        TCGA-BR-A4J8        TCGA-BR-A4J9 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-BR-A4PF        TCGA-BR-A4QI        TCGA-BR-A4QL        TCGA-CD-5798 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-CD-5799        TCGA-CD-5800        TCGA-CD-5801        TCGA-CD-5802 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-CD-5803        TCGA-CG-4300        TCGA-CG-4301        TCGA-CG-4304 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-CG-4305        TCGA-CG-4306        TCGA-CG-4436        TCGA-CG-4437 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-CG-4438        TCGA-CG-4440        TCGA-CG-4441        TCGA-CG-4443 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-CG-4444        TCGA-CG-4449        TCGA-CG-4455        TCGA-CG-4460 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-CG-4462        TCGA-CG-4465        TCGA-CG-4466        TCGA-CG-4469 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-CG-4472        TCGA-CG-4474        TCGA-CG-4477        TCGA-CG-5716 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-CG-5717        TCGA-CG-5718        TCGA-CG-5719        TCGA-CG-5720 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-CG-5721        TCGA-CG-5722        TCGA-CG-5723        TCGA-CG-5724 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-CG-5725        TCGA-CG-5726        TCGA-CG-5727        TCGA-CG-5728 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-CG-5730        TCGA-CG-5732        TCGA-CG-5733        TCGA-CG-5734 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-D7-5577        TCGA-D7-5578        TCGA-D7-5579        TCGA-D7-6518 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-D7-6519        TCGA-D7-6520        TCGA-D7-6521        TCGA-D7-6522 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-D7-6524        TCGA-D7-6525        TCGA-D7-6526        TCGA-D7-6527 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-D7-6528        TCGA-D7-6815        TCGA-D7-6817        TCGA-D7-6818 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-D7-6820        TCGA-D7-6822        TCGA-EQ-5647        TCGA-EQ-8122 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-F1-6177        TCGA-F1-6874        TCGA-F1-6875        TCGA-FP-7735 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-FP-7829        TCGA-FP-7916        TCGA-FP-7998        TCGA-FP-8099 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-FP-8209        TCGA-FP-8210        TCGA-FP-8631        TCGA-HJ-7597 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-IN-7806        TCGA-IN-7808        TCGA-IP-7968 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
[1] "Remove cluster labels:" "3P GAIN CNV"           
clus
      3P GAIN CNV 3P GAIN WILD-TYPE 
                1               142 
       TCGA-B7-5816        TCGA-B7-5818        TCGA-BR-6452        TCGA-BR-6455 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-BR-6457        TCGA-BR-6458        TCGA-BR-6563        TCGA-BR-6564 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-BR-6565        TCGA-BR-6566        TCGA-BR-6705        TCGA-BR-6706 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-BR-6707        TCGA-BR-6709        TCGA-BR-6710        TCGA-BR-6801 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-BR-6802        TCGA-BR-6803        TCGA-BR-6852        TCGA-BR-7196 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-BR-7197        TCGA-BR-7703        TCGA-BR-7704        TCGA-BR-7707 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-BR-7715        TCGA-BR-7716        TCGA-BR-7717        TCGA-BR-7723 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-BR-7851        TCGA-BR-7901        TCGA-BR-7957        TCGA-BR-7958 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-BR-7959        TCGA-BR-8059        TCGA-BR-8060        TCGA-BR-8077 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-BR-8078        TCGA-BR-8080        TCGA-BR-8081        TCGA-BR-8284 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-BR-8285        TCGA-BR-8286        TCGA-BR-8289        TCGA-BR-8291 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-BR-8295        TCGA-BR-8296        TCGA-BR-8297        TCGA-BR-8592 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-BR-A4IU        TCGA-BR-A4IV        TCGA-BR-A4IY        TCGA-BR-A4IZ 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-BR-A4J1        TCGA-BR-A4J2        TCGA-BR-A4J4        TCGA-BR-A4J5 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-BR-A4J6        TCGA-BR-A4J8        TCGA-BR-A4J9        TCGA-BR-A4PF 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-BR-A4QI        TCGA-BR-A4QL        TCGA-CD-5798        TCGA-CD-5799 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-CD-5800        TCGA-CD-5801        TCGA-CD-5802        TCGA-CD-5803 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-CG-4300        TCGA-CG-4301        TCGA-CG-4304        TCGA-CG-4305 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-CG-4306        TCGA-CG-4436        TCGA-CG-4437        TCGA-CG-4438 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-CG-4440        TCGA-CG-4441        TCGA-CG-4443        TCGA-CG-4444 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-CG-4449        TCGA-CG-4455        TCGA-CG-4460        TCGA-CG-4462 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-CG-4465        TCGA-CG-4466        TCGA-CG-4469        TCGA-CG-4472 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-CG-4474        TCGA-CG-4477        TCGA-CG-5716        TCGA-CG-5717 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-CG-5718        TCGA-CG-5719        TCGA-CG-5720        TCGA-CG-5721 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-CG-5722        TCGA-CG-5723        TCGA-CG-5724        TCGA-CG-5725 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-CG-5726        TCGA-CG-5727        TCGA-CG-5728        TCGA-CG-5730 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-CG-5732        TCGA-CG-5733        TCGA-CG-5734        TCGA-D7-5577 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-D7-5578        TCGA-D7-5579        TCGA-D7-6518        TCGA-D7-6519 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-D7-6520        TCGA-D7-6521        TCGA-D7-6522        TCGA-D7-6524 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-D7-6525        TCGA-D7-6526        TCGA-D7-6527        TCGA-D7-6528 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-D7-6815        TCGA-D7-6817        TCGA-D7-6818        TCGA-D7-6820 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-D7-6822        TCGA-EQ-5647        TCGA-EQ-8122        TCGA-F1-6177 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-F1-6874        TCGA-F1-6875        TCGA-FP-7735        TCGA-FP-7829 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-FP-7916        TCGA-FP-7998        TCGA-FP-8099        TCGA-FP-8209 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-FP-8210        TCGA-FP-8631        TCGA-HJ-7597        TCGA-IN-7806 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-IN-7808        TCGA-IP-7968 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
D5V2, continuous
D5V3, binary
[1] "tbl2"
                   cls
clus                [,1] [,2]
  3P GAIN CNV          1    2
  3P GAIN WILD-TYPE   71  106
        clus
vv       3P GAIN CNV 3P GAIN WILD-TYPE
  FEMALE           1                71
  MALE             2               106
                   vv
clus                STOMACH  ADENOCARCINOMA  DIFFUSE TYPE
  3P GAIN CNV                                           0
  3P GAIN WILD-TYPE                                    10
                   vv
clus                STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  3P GAIN CNV                                                            0
  3P GAIN WILD-TYPE                                                     16
                   vv
clus                STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  3P GAIN CNV                                                                       0
  3P GAIN WILD-TYPE                                                                 8
                   vv
clus                STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE
  3P GAIN CNV                                                              0
  3P GAIN WILD-TYPE                                                        3
                   vv
clus                STOMACH ADENOCARCINOMA  SIGNET RING TYPE
  3P GAIN CNV                                              0
  3P GAIN WILD-TYPE                                        1
                   vv
clus                STOMACH ADENOCARCINOMA - DIFFUSE TYPE
  3P GAIN CNV                                           0
  3P GAIN WILD-TYPE                                    16
                   vv
clus                STOMACH ADENOCARCINOMA - NOT OTHERWISE SPECIFIED (NOS)
  3P GAIN CNV                                                            3
  3P GAIN WILD-TYPE                                                     70
                   vv
clus                STOMACH INTESTINAL ADENOCARCINOMA - MUCINOUS TYPE
  3P GAIN CNV                                                       0
  3P GAIN WILD-TYPE                                                 7
                   vv
clus                STOMACH INTESTINAL ADENOCARCINOMA - PAPILLARY TYPE
  3P GAIN CNV                                                        0
  3P GAIN WILD-TYPE                                                  3
                   vv
clus                STOMACH INTESTINAL ADENOCARCINOMA - TUBULAR TYPE
  3P GAIN CNV                                                      0
  3P GAIN WILD-TYPE                                               10
                   vv
clus                STOMACH INTESTINAL ADENOCARCINOMA - TYPE NOT OTHERWISE SPECIFIED (NOS)
  3P GAIN CNV                                                                            0
  3P GAIN WILD-TYPE                                                                     28
D5V4, multiclass
                   vv
clus                T1 T2 T3 T4
  3P GAIN CNV        0  1  1  1
  3P GAIN WILD-TYPE  6 51 55 17
D5V5, multiclass
    clus
vv   3P GAIN CNV 3P GAIN WILD-TYPE
  T1           0                 6
  T2           1                51
  T3           1                55
  T4           1                17
                   vv
clus                N0 N1 N2 N3
  3P GAIN CNV        1  1  1  0
  3P GAIN WILD-TYPE 43 48 22 15
D5V6, multiclass
    clus
vv   3P GAIN CNV 3P GAIN WILD-TYPE
  N0           1                43
  N1           1                48
  N2           1                22
  N3           0                15
                   vv
clus                 M0  M1  MX
  3P GAIN CNV         3   0   0
  3P GAIN WILD-TYPE 115  16   8
D5V7, multiclass
    clus
vv   3P GAIN CNV 3P GAIN WILD-TYPE
  M0           3               115
  M1           0                16
  MX           0                 8
                   vv
clus                 I II III IV
  3P GAIN CNV        1  0   1  1
  3P GAIN WILD-TYPE 23 37  38 25
D5V8, multiclass
     clus
vv    3P GAIN CNV 3P GAIN WILD-TYPE
  I             1                23
  II            0                37
  III           1                38
  IV            1                25
D5V9, binary
[1] "tbl2"
                   cls
clus                [,1] [,2]
  3P GAIN CNV          0    3
  3P GAIN WILD-TYPE    5  172
     clus
vv    3P GAIN CNV 3P GAIN WILD-TYPE
  NO            0                 5
  YES           3               172
                   vv
clus                 R0  R1  R2  RX
  3P GAIN CNV         1   0   0   2
  3P GAIN WILD-TYPE 124   7  12  23
D5V10, multiclass
    clus
vv   3P GAIN CNV 3P GAIN WILD-TYPE
  R0           1               124
  R1           0                 7
  R2           0                12
  RX           2                23
D5V11, continuous

Clustering(6) Variable = 3q gain
D6V1, survival
                   sevent
clus2                 0   1
  3Q GAIN CNV        11   0
  3Q GAIN WILD-TYPE 113  19
      3Q GAIN CNV 3Q GAIN WILD-TYPE 
               11               132 
      3Q GAIN CNV 3Q GAIN WILD-TYPE 
                0                19 
$`3Q GAIN CNV`
TCGA-B7-5818 TCGA-BR-6565 TCGA-BR-7722 TCGA-BR-7723 TCGA-BR-8295 TCGA-BR-A4J4 
        0.10         0.62         0.16         4.54         1.55         0.53 
TCGA-CD-5799 TCGA-CD-5801 TCGA-CG-4305 TCGA-CG-4472 TCGA-D7-6521 
        0.69         0.49        15.95        12.00         8.19 

$`3Q GAIN WILD-TYPE`
TCGA-B7-5816 TCGA-BR-6452 TCGA-BR-6455 TCGA-BR-6457 TCGA-BR-6458 TCGA-BR-6563 
        5.62         0.95         1.41         1.35         1.35         0.85 
TCGA-BR-6564 TCGA-BR-6566 TCGA-BR-6705 TCGA-BR-6706 TCGA-BR-6707 TCGA-BR-6709 
        0.82         0.62         1.71         2.17         0.99         1.22 
TCGA-BR-6710 TCGA-BR-6801 TCGA-BR-6802 TCGA-BR-6803 TCGA-BR-6852 TCGA-BR-7196 
        0.66         1.12         0.76         0.66         0.26         1.22 
TCGA-BR-7197 TCGA-BR-7703 TCGA-BR-7704 TCGA-BR-7707 TCGA-BR-7715 TCGA-BR-7716 
        1.48         0.46         1.25         0.13         1.05         0.82 
TCGA-BR-7717 TCGA-BR-7851 TCGA-BR-7901 TCGA-BR-7957 TCGA-BR-7958 TCGA-BR-7959 
        0.69         0.99         0.95         0.69         0.16         1.08 
TCGA-BR-8059 TCGA-BR-8060 TCGA-BR-8077 TCGA-BR-8078 TCGA-BR-8080 TCGA-BR-8081 
        0.82         1.32         0.69         0.95         0.49         0.46 
TCGA-BR-8284 TCGA-BR-8285 TCGA-BR-8286 TCGA-BR-8289 TCGA-BR-8291 TCGA-BR-8296 
        0.72         0.26         0.43         0.26         1.18         1.48 
TCGA-BR-8297 TCGA-BR-8592 TCGA-BR-A4IU TCGA-BR-A4IV TCGA-BR-A4IY TCGA-BR-A4IZ 
        0.76         0.20         0.59         0.92         0.39         0.79 
TCGA-BR-A4J1 TCGA-BR-A4J2 TCGA-BR-A4J5 TCGA-BR-A4J6 TCGA-BR-A4J8 TCGA-BR-A4J9 
        0.72         0.79         0.43         0.13         0.23         0.10 
TCGA-BR-A4PF TCGA-BR-A4QI TCGA-BR-A4QL TCGA-CD-5798 TCGA-CD-5800 TCGA-CD-5802 
        0.72         0.49         2.24         0.82         0.36         0.30 
TCGA-CD-5803 TCGA-CG-4300 TCGA-CG-4301 TCGA-CG-4304 TCGA-CG-4306 TCGA-CG-4436 
        0.07        20.02         3.02        27.02         1.02        52.96 
TCGA-CG-4437 TCGA-CG-4438 TCGA-CG-4440 TCGA-CG-4441 TCGA-CG-4443 TCGA-CG-4444 
        8.05        54.05         4.01        14.01        29.98        47.05 
TCGA-CG-4449 TCGA-CG-4455 TCGA-CG-4460 TCGA-CG-4462 TCGA-CG-4465 TCGA-CG-4466 
       19.07        12.03        21.99         1.02         8.98        18.94 
TCGA-CG-4469 TCGA-CG-4474 TCGA-CG-4477 TCGA-CG-5716 TCGA-CG-5717 TCGA-CG-5718 
        7.07         1.02         1.02         1.02         6.94         1.02 
TCGA-CG-5719 TCGA-CG-5720 TCGA-CG-5721 TCGA-CG-5722 TCGA-CG-5723 TCGA-CG-5724 
        1.02         0.99         5.98         0.95        70.06        12.03 
TCGA-CG-5725 TCGA-CG-5726 TCGA-CG-5727 TCGA-CG-5728 TCGA-CG-5730 TCGA-CG-5732 
       15.02        28.96        31.04        65.10         4.01        55.04 
TCGA-CG-5733 TCGA-CG-5734 TCGA-D7-5577 TCGA-D7-5578 TCGA-D7-5579 TCGA-D7-6518 
       21.07         7.99         8.65         3.58         4.54         9.80 
TCGA-D7-6519 TCGA-D7-6520 TCGA-D7-6522 TCGA-D7-6524 TCGA-D7-6525 TCGA-D7-6526 
       15.65         9.63         6.90         0.69         5.95         6.61 
TCGA-D7-6527 TCGA-D7-6528 TCGA-D7-6815 TCGA-D7-6817 TCGA-D7-6818 TCGA-D7-6820 
        4.14         1.68         3.65         4.70         4.04         2.93 
TCGA-D7-6822 TCGA-EQ-5647 TCGA-EQ-8122 TCGA-F1-6177 TCGA-F1-6874 TCGA-F1-6875 
        4.27         0.62         7.79         6.54         2.01        72.23 
TCGA-FP-7735 TCGA-FP-7829 TCGA-FP-7916 TCGA-FP-7998 TCGA-FP-8099 TCGA-FP-8209 
        0.39         0.20         3.02         3.58         1.02        59.05 
TCGA-FP-8210 TCGA-FP-8631 TCGA-HJ-7597 TCGA-IN-7806 TCGA-IN-7808 TCGA-IP-7968 
        5.03         0.56        26.43         6.87         3.55         2.53 

      3Q GAIN CNV 3Q GAIN WILD-TYPE 
             0.10              0.07 
      3Q GAIN CNV 3Q GAIN WILD-TYPE 
            15.95             72.23 
      3Q GAIN CNV 3Q GAIN WILD-TYPE 
            0.690             1.285 
[1] "0.1 - 15.9 (0.7)" "0.1 - 72.2 (1.3)"
       TCGA-B7-5816        TCGA-B7-5818        TCGA-BR-6452        TCGA-BR-6455 
"3Q GAIN WILD-TYPE"       "3Q GAIN CNV" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" 
       TCGA-BR-6457        TCGA-BR-6458        TCGA-BR-6563        TCGA-BR-6564 
"3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" 
       TCGA-BR-6565        TCGA-BR-6566        TCGA-BR-6705        TCGA-BR-6706 
      "3Q GAIN CNV" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" 
       TCGA-BR-6707        TCGA-BR-6709        TCGA-BR-6710        TCGA-BR-6801 
"3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" 
       TCGA-BR-6802        TCGA-BR-6803        TCGA-BR-6852        TCGA-BR-7196 
"3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" 
       TCGA-BR-7197        TCGA-BR-7703        TCGA-BR-7704        TCGA-BR-7707 
"3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" 
       TCGA-BR-7715        TCGA-BR-7716        TCGA-BR-7717        TCGA-BR-7722 
"3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE"       "3Q GAIN CNV" 
       TCGA-BR-7723        TCGA-BR-7851        TCGA-BR-7901        TCGA-BR-7957 
      "3Q GAIN CNV" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" 
       TCGA-BR-7958        TCGA-BR-7959        TCGA-BR-8059        TCGA-BR-8060 
"3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" 
       TCGA-BR-8077        TCGA-BR-8078        TCGA-BR-8080        TCGA-BR-8081 
"3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" 
       TCGA-BR-8284        TCGA-BR-8285        TCGA-BR-8286        TCGA-BR-8289 
"3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" 
       TCGA-BR-8291        TCGA-BR-8295        TCGA-BR-8296        TCGA-BR-8297 
"3Q GAIN WILD-TYPE"       "3Q GAIN CNV" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" 
       TCGA-BR-8592        TCGA-BR-A4IU        TCGA-BR-A4IV        TCGA-BR-A4IY 
"3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" 
       TCGA-BR-A4IZ        TCGA-BR-A4J1        TCGA-BR-A4J2        TCGA-BR-A4J4 
"3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE"       "3Q GAIN CNV" 
       TCGA-BR-A4J5        TCGA-BR-A4J6        TCGA-BR-A4J8        TCGA-BR-A4J9 
"3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" 
       TCGA-BR-A4PF        TCGA-BR-A4QI        TCGA-BR-A4QL        TCGA-CD-5798 
"3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" 
       TCGA-CD-5799        TCGA-CD-5800        TCGA-CD-5801        TCGA-CD-5802 
      "3Q GAIN CNV" "3Q GAIN WILD-TYPE"       "3Q GAIN CNV" "3Q GAIN WILD-TYPE" 
       TCGA-CD-5803        TCGA-CG-4300        TCGA-CG-4301        TCGA-CG-4304 
"3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" 
       TCGA-CG-4305        TCGA-CG-4306        TCGA-CG-4436        TCGA-CG-4437 
      "3Q GAIN CNV" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" 
       TCGA-CG-4438        TCGA-CG-4440        TCGA-CG-4441        TCGA-CG-4443 
"3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" 
       TCGA-CG-4444        TCGA-CG-4449        TCGA-CG-4455        TCGA-CG-4460 
"3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" 
       TCGA-CG-4462        TCGA-CG-4465        TCGA-CG-4466        TCGA-CG-4469 
"3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" 
       TCGA-CG-4472        TCGA-CG-4474        TCGA-CG-4477        TCGA-CG-5716 
      "3Q GAIN CNV" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" 
       TCGA-CG-5717        TCGA-CG-5718        TCGA-CG-5719        TCGA-CG-5720 
"3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" 
       TCGA-CG-5721        TCGA-CG-5722        TCGA-CG-5723        TCGA-CG-5724 
"3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" 
       TCGA-CG-5725        TCGA-CG-5726        TCGA-CG-5727        TCGA-CG-5728 
"3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" 
       TCGA-CG-5730        TCGA-CG-5732        TCGA-CG-5733        TCGA-CG-5734 
"3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" 
       TCGA-D7-5577        TCGA-D7-5578        TCGA-D7-5579        TCGA-D7-6518 
"3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" 
       TCGA-D7-6519        TCGA-D7-6520        TCGA-D7-6521        TCGA-D7-6522 
"3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE"       "3Q GAIN CNV" "3Q GAIN WILD-TYPE" 
       TCGA-D7-6524        TCGA-D7-6525        TCGA-D7-6526        TCGA-D7-6527 
"3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" 
       TCGA-D7-6528        TCGA-D7-6815        TCGA-D7-6817        TCGA-D7-6818 
"3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" 
       TCGA-D7-6820        TCGA-D7-6822        TCGA-EQ-5647        TCGA-EQ-8122 
"3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" 
       TCGA-F1-6177        TCGA-F1-6874        TCGA-F1-6875        TCGA-FP-7735 
"3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" 
       TCGA-FP-7829        TCGA-FP-7916        TCGA-FP-7998        TCGA-FP-8099 
"3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" 
       TCGA-FP-8209        TCGA-FP-8210        TCGA-FP-8631        TCGA-HJ-7597 
"3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" 
       TCGA-IN-7806        TCGA-IN-7808        TCGA-IP-7968 
"3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" 
       TCGA-B7-5816        TCGA-B7-5818        TCGA-BR-6452        TCGA-BR-6455 
"3Q GAIN WILD-TYPE"       "3Q GAIN CNV" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" 
       TCGA-BR-6457        TCGA-BR-6458        TCGA-BR-6563        TCGA-BR-6564 
"3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" 
       TCGA-BR-6565        TCGA-BR-6566        TCGA-BR-6705        TCGA-BR-6706 
      "3Q GAIN CNV" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" 
       TCGA-BR-6707        TCGA-BR-6709        TCGA-BR-6710        TCGA-BR-6801 
"3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" 
       TCGA-BR-6802        TCGA-BR-6803        TCGA-BR-6852        TCGA-BR-7196 
"3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" 
       TCGA-BR-7197        TCGA-BR-7703        TCGA-BR-7704        TCGA-BR-7707 
"3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" 
       TCGA-BR-7715        TCGA-BR-7716        TCGA-BR-7717        TCGA-BR-7722 
"3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE"       "3Q GAIN CNV" 
       TCGA-BR-7723        TCGA-BR-7851        TCGA-BR-7901        TCGA-BR-7957 
      "3Q GAIN CNV" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" 
       TCGA-BR-7958        TCGA-BR-7959        TCGA-BR-8059        TCGA-BR-8060 
"3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" 
       TCGA-BR-8077        TCGA-BR-8078        TCGA-BR-8080        TCGA-BR-8081 
"3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" 
       TCGA-BR-8284        TCGA-BR-8285        TCGA-BR-8286        TCGA-BR-8289 
"3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" 
       TCGA-BR-8291        TCGA-BR-8295        TCGA-BR-8296        TCGA-BR-8297 
"3Q GAIN WILD-TYPE"       "3Q GAIN CNV" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" 
       TCGA-BR-8592        TCGA-BR-A4IU        TCGA-BR-A4IV        TCGA-BR-A4IY 
"3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" 
       TCGA-BR-A4IZ        TCGA-BR-A4J1        TCGA-BR-A4J2        TCGA-BR-A4J4 
"3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE"       "3Q GAIN CNV" 
       TCGA-BR-A4J5        TCGA-BR-A4J6        TCGA-BR-A4J8        TCGA-BR-A4J9 
"3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" 
       TCGA-BR-A4PF        TCGA-BR-A4QI        TCGA-BR-A4QL        TCGA-CD-5798 
"3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" 
       TCGA-CD-5799        TCGA-CD-5800        TCGA-CD-5801        TCGA-CD-5802 
      "3Q GAIN CNV" "3Q GAIN WILD-TYPE"       "3Q GAIN CNV" "3Q GAIN WILD-TYPE" 
       TCGA-CD-5803        TCGA-CG-4300        TCGA-CG-4301        TCGA-CG-4304 
"3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" 
       TCGA-CG-4305        TCGA-CG-4306        TCGA-CG-4436        TCGA-CG-4437 
      "3Q GAIN CNV" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" 
       TCGA-CG-4438        TCGA-CG-4440        TCGA-CG-4441        TCGA-CG-4443 
"3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" 
       TCGA-CG-4444        TCGA-CG-4449        TCGA-CG-4455        TCGA-CG-4460 
"3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" 
       TCGA-CG-4462        TCGA-CG-4465        TCGA-CG-4466        TCGA-CG-4469 
"3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" 
       TCGA-CG-4472        TCGA-CG-4474        TCGA-CG-4477        TCGA-CG-5716 
      "3Q GAIN CNV" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" 
       TCGA-CG-5717        TCGA-CG-5718        TCGA-CG-5719        TCGA-CG-5720 
"3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" 
       TCGA-CG-5721        TCGA-CG-5722        TCGA-CG-5723        TCGA-CG-5724 
"3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" 
       TCGA-CG-5725        TCGA-CG-5726        TCGA-CG-5727        TCGA-CG-5728 
"3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" 
       TCGA-CG-5730        TCGA-CG-5732        TCGA-CG-5733        TCGA-CG-5734 
"3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" 
       TCGA-D7-5577        TCGA-D7-5578        TCGA-D7-5579        TCGA-D7-6518 
"3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" 
       TCGA-D7-6519        TCGA-D7-6520        TCGA-D7-6521        TCGA-D7-6522 
"3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE"       "3Q GAIN CNV" "3Q GAIN WILD-TYPE" 
       TCGA-D7-6524        TCGA-D7-6525        TCGA-D7-6526        TCGA-D7-6527 
"3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" 
       TCGA-D7-6528        TCGA-D7-6815        TCGA-D7-6817        TCGA-D7-6818 
"3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" 
       TCGA-D7-6820        TCGA-D7-6822        TCGA-EQ-5647        TCGA-EQ-8122 
"3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" 
       TCGA-F1-6177        TCGA-F1-6874        TCGA-F1-6875        TCGA-FP-7735 
"3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" 
       TCGA-FP-7829        TCGA-FP-7916        TCGA-FP-7998        TCGA-FP-8099 
"3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" 
       TCGA-FP-8209        TCGA-FP-8210        TCGA-FP-8631        TCGA-HJ-7597 
"3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" 
       TCGA-IN-7806        TCGA-IN-7808        TCGA-IP-7968 
"3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" 
       TCGA-B7-5816        TCGA-B7-5818        TCGA-BR-6452        TCGA-BR-6455 
"3Q GAIN WILD-TYPE"       "3Q GAIN CNV" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" 
       TCGA-BR-6457        TCGA-BR-6458        TCGA-BR-6563        TCGA-BR-6564 
"3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" 
       TCGA-BR-6565        TCGA-BR-6566        TCGA-BR-6705        TCGA-BR-6706 
      "3Q GAIN CNV" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" 
       TCGA-BR-6707        TCGA-BR-6709        TCGA-BR-6710        TCGA-BR-6801 
"3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" 
       TCGA-BR-6802        TCGA-BR-6803        TCGA-BR-6852        TCGA-BR-7196 
"3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" 
       TCGA-BR-7197        TCGA-BR-7703        TCGA-BR-7704        TCGA-BR-7707 
"3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" 
       TCGA-BR-7715        TCGA-BR-7716        TCGA-BR-7717        TCGA-BR-7722 
"3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE"       "3Q GAIN CNV" 
       TCGA-BR-7723        TCGA-BR-7851        TCGA-BR-7901        TCGA-BR-7957 
      "3Q GAIN CNV" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" 
       TCGA-BR-7958        TCGA-BR-7959        TCGA-BR-8059        TCGA-BR-8060 
"3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" 
       TCGA-BR-8077        TCGA-BR-8078        TCGA-BR-8080        TCGA-BR-8081 
"3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" 
       TCGA-BR-8284        TCGA-BR-8285        TCGA-BR-8286        TCGA-BR-8289 
"3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" 
       TCGA-BR-8291        TCGA-BR-8295        TCGA-BR-8296        TCGA-BR-8297 
"3Q GAIN WILD-TYPE"       "3Q GAIN CNV" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" 
       TCGA-BR-8592        TCGA-BR-A4IU        TCGA-BR-A4IV        TCGA-BR-A4IY 
"3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" 
       TCGA-BR-A4IZ        TCGA-BR-A4J1        TCGA-BR-A4J2        TCGA-BR-A4J4 
"3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE"       "3Q GAIN CNV" 
       TCGA-BR-A4J5        TCGA-BR-A4J6        TCGA-BR-A4J8        TCGA-BR-A4J9 
"3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" 
       TCGA-BR-A4PF        TCGA-BR-A4QI        TCGA-BR-A4QL        TCGA-CD-5798 
"3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" 
       TCGA-CD-5799        TCGA-CD-5800        TCGA-CD-5801        TCGA-CD-5802 
      "3Q GAIN CNV" "3Q GAIN WILD-TYPE"       "3Q GAIN CNV" "3Q GAIN WILD-TYPE" 
       TCGA-CD-5803        TCGA-CG-4300        TCGA-CG-4301        TCGA-CG-4304 
"3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" 
       TCGA-CG-4305        TCGA-CG-4306        TCGA-CG-4436        TCGA-CG-4437 
      "3Q GAIN CNV" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" 
       TCGA-CG-4438        TCGA-CG-4440        TCGA-CG-4441        TCGA-CG-4443 
"3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" 
       TCGA-CG-4444        TCGA-CG-4449        TCGA-CG-4455        TCGA-CG-4460 
"3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" 
       TCGA-CG-4462        TCGA-CG-4465        TCGA-CG-4466        TCGA-CG-4469 
"3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" 
       TCGA-CG-4472        TCGA-CG-4474        TCGA-CG-4477        TCGA-CG-5716 
      "3Q GAIN CNV" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" 
       TCGA-CG-5717        TCGA-CG-5718        TCGA-CG-5719        TCGA-CG-5720 
"3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" 
       TCGA-CG-5721        TCGA-CG-5722        TCGA-CG-5723        TCGA-CG-5724 
"3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" 
       TCGA-CG-5725        TCGA-CG-5726        TCGA-CG-5727        TCGA-CG-5728 
"3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" 
       TCGA-CG-5730        TCGA-CG-5732        TCGA-CG-5733        TCGA-CG-5734 
"3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" 
       TCGA-D7-5577        TCGA-D7-5578        TCGA-D7-5579        TCGA-D7-6518 
"3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" 
       TCGA-D7-6519        TCGA-D7-6520        TCGA-D7-6521        TCGA-D7-6522 
"3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE"       "3Q GAIN CNV" "3Q GAIN WILD-TYPE" 
       TCGA-D7-6524        TCGA-D7-6525        TCGA-D7-6526        TCGA-D7-6527 
"3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" 
       TCGA-D7-6528        TCGA-D7-6815        TCGA-D7-6817        TCGA-D7-6818 
"3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" 
       TCGA-D7-6820        TCGA-D7-6822        TCGA-EQ-5647        TCGA-EQ-8122 
"3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" 
       TCGA-F1-6177        TCGA-F1-6874        TCGA-F1-6875        TCGA-FP-7735 
"3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" 
       TCGA-FP-7829        TCGA-FP-7916        TCGA-FP-7998        TCGA-FP-8099 
"3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" 
       TCGA-FP-8209        TCGA-FP-8210        TCGA-FP-8631        TCGA-HJ-7597 
"3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" 
       TCGA-IN-7806        TCGA-IN-7808        TCGA-IP-7968 
"3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" 
[1] "hr="     "2.7e+07"
D6V2, continuous
D6V3, binary
[1] "tbl2"
                   cls
clus                [,1] [,2]
  3Q GAIN CNV          2   13
  3Q GAIN WILD-TYPE   70   95
        clus
vv       3Q GAIN CNV 3Q GAIN WILD-TYPE
  FEMALE           2                70
  MALE            13                95
                   vv
clus                STOMACH  ADENOCARCINOMA  DIFFUSE TYPE
  3Q GAIN CNV                                           0
  3Q GAIN WILD-TYPE                                    10
                   vv
clus                STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  3Q GAIN CNV                                                            2
  3Q GAIN WILD-TYPE                                                     14
                   vv
clus                STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  3Q GAIN CNV                                                                       0
  3Q GAIN WILD-TYPE                                                                 8
                   vv
clus                STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE
  3Q GAIN CNV                                                              0
  3Q GAIN WILD-TYPE                                                        3
                   vv
clus                STOMACH ADENOCARCINOMA  SIGNET RING TYPE
  3Q GAIN CNV                                              0
  3Q GAIN WILD-TYPE                                        1
                   vv
clus                STOMACH ADENOCARCINOMA - DIFFUSE TYPE
  3Q GAIN CNV                                           3
  3Q GAIN WILD-TYPE                                    13
                   vv
clus                STOMACH ADENOCARCINOMA - NOT OTHERWISE SPECIFIED (NOS)
  3Q GAIN CNV                                                            8
  3Q GAIN WILD-TYPE                                                     65
                   vv
clus                STOMACH INTESTINAL ADENOCARCINOMA - MUCINOUS TYPE
  3Q GAIN CNV                                                       0
  3Q GAIN WILD-TYPE                                                 7
                   vv
clus                STOMACH INTESTINAL ADENOCARCINOMA - PAPILLARY TYPE
  3Q GAIN CNV                                                        0
  3Q GAIN WILD-TYPE                                                  3
                   vv
clus                STOMACH INTESTINAL ADENOCARCINOMA - TUBULAR TYPE
  3Q GAIN CNV                                                      0
  3Q GAIN WILD-TYPE                                               10
                   vv
clus                STOMACH INTESTINAL ADENOCARCINOMA - TYPE NOT OTHERWISE SPECIFIED (NOS)
  3Q GAIN CNV                                                                            1
  3Q GAIN WILD-TYPE                                                                     27
D6V4, multiclass
                   vv
clus                T1 T2 T3 T4
  3Q GAIN CNV        0  5  5  3
  3Q GAIN WILD-TYPE  6 47 51 15
D6V5, multiclass
    clus
vv   3Q GAIN CNV 3Q GAIN WILD-TYPE
  T1           0                 6
  T2           5                47
  T3           5                51
  T4           3                15
                   vv
clus                N0 N1 N2 N3
  3Q GAIN CNV        3  5  3  1
  3Q GAIN WILD-TYPE 41 44 20 14
D6V6, multiclass
    clus
vv   3Q GAIN CNV 3Q GAIN WILD-TYPE
  N0           3                41
  N1           5                44
  N2           3                20
  N3           1                14
                   vv
clus                 M0  M1  MX
  3Q GAIN CNV        12   0   1
  3Q GAIN WILD-TYPE 106  16   7
D6V7, multiclass
    clus
vv   3Q GAIN CNV 3Q GAIN WILD-TYPE
  M0          12               106
  M1           0                16
  MX           1                 7
                   vv
clus                 I II III IV
  3Q GAIN CNV        2  4   4  2
  3Q GAIN WILD-TYPE 22 33  35 24
D6V8, multiclass
     clus
vv    3Q GAIN CNV 3Q GAIN WILD-TYPE
  I             2                22
  II            4                33
  III           4                35
  IV            2                24
D6V9, binary
[1] "tbl2"
                   cls
clus                [,1] [,2]
  3Q GAIN CNV          0   15
  3Q GAIN WILD-TYPE    5  160
     clus
vv    3Q GAIN CNV 3Q GAIN WILD-TYPE
  NO            0                 5
  YES          15               160
                   vv
clus                 R0  R1  R2  RX
  3Q GAIN CNV        10   0   0   3
  3Q GAIN WILD-TYPE 115   7  12  22
D6V10, multiclass
    clus
vv   3Q GAIN CNV 3Q GAIN WILD-TYPE
  R0          10               115
  R1           0                 7
  R2           0                12
  RX           3                22
D6V11, continuous

Clustering(7) Variable = 4p gain
D7V1, survival
                   sevent
clus2                 0   1
  4P GAIN CNV         2   0
  4P GAIN WILD-TYPE 122  19
      4P GAIN CNV 4P GAIN WILD-TYPE 
                2               141 
      4P GAIN CNV 4P GAIN WILD-TYPE 
                0                19 
$`4P GAIN CNV`
TCGA-CG-4443 TCGA-D7-5579 
       29.98         4.54 

$`4P GAIN WILD-TYPE`
TCGA-B7-5816 TCGA-B7-5818 TCGA-BR-6452 TCGA-BR-6455 TCGA-BR-6457 TCGA-BR-6458 
        5.62         0.10         0.95         1.41         1.35         1.35 
TCGA-BR-6563 TCGA-BR-6564 TCGA-BR-6565 TCGA-BR-6566 TCGA-BR-6705 TCGA-BR-6706 
        0.85         0.82         0.62         0.62         1.71         2.17 
TCGA-BR-6707 TCGA-BR-6709 TCGA-BR-6710 TCGA-BR-6801 TCGA-BR-6802 TCGA-BR-6803 
        0.99         1.22         0.66         1.12         0.76         0.66 
TCGA-BR-6852 TCGA-BR-7196 TCGA-BR-7197 TCGA-BR-7703 TCGA-BR-7704 TCGA-BR-7707 
        0.26         1.22         1.48         0.46         1.25         0.13 
TCGA-BR-7715 TCGA-BR-7716 TCGA-BR-7717 TCGA-BR-7722 TCGA-BR-7723 TCGA-BR-7851 
        1.05         0.82         0.69         0.16         4.54         0.99 
TCGA-BR-7901 TCGA-BR-7957 TCGA-BR-7958 TCGA-BR-7959 TCGA-BR-8059 TCGA-BR-8060 
        0.95         0.69         0.16         1.08         0.82         1.32 
TCGA-BR-8077 TCGA-BR-8078 TCGA-BR-8080 TCGA-BR-8081 TCGA-BR-8284 TCGA-BR-8285 
        0.69         0.95         0.49         0.46         0.72         0.26 
TCGA-BR-8286 TCGA-BR-8289 TCGA-BR-8291 TCGA-BR-8295 TCGA-BR-8296 TCGA-BR-8297 
        0.43         0.26         1.18         1.55         1.48         0.76 
TCGA-BR-8592 TCGA-BR-A4IU TCGA-BR-A4IV TCGA-BR-A4IY TCGA-BR-A4IZ TCGA-BR-A4J1 
        0.20         0.59         0.92         0.39         0.79         0.72 
TCGA-BR-A4J2 TCGA-BR-A4J4 TCGA-BR-A4J5 TCGA-BR-A4J6 TCGA-BR-A4J8 TCGA-BR-A4J9 
        0.79         0.53         0.43         0.13         0.23         0.10 
TCGA-BR-A4PF TCGA-BR-A4QI TCGA-BR-A4QL TCGA-CD-5798 TCGA-CD-5799 TCGA-CD-5800 
        0.72         0.49         2.24         0.82         0.69         0.36 
TCGA-CD-5801 TCGA-CD-5802 TCGA-CD-5803 TCGA-CG-4300 TCGA-CG-4301 TCGA-CG-4304 
        0.49         0.30         0.07        20.02         3.02        27.02 
TCGA-CG-4305 TCGA-CG-4306 TCGA-CG-4436 TCGA-CG-4437 TCGA-CG-4438 TCGA-CG-4440 
       15.95         1.02        52.96         8.05        54.05         4.01 
TCGA-CG-4441 TCGA-CG-4444 TCGA-CG-4449 TCGA-CG-4455 TCGA-CG-4460 TCGA-CG-4462 
       14.01        47.05        19.07        12.03        21.99         1.02 
TCGA-CG-4465 TCGA-CG-4466 TCGA-CG-4469 TCGA-CG-4472 TCGA-CG-4474 TCGA-CG-4477 
        8.98        18.94         7.07        12.00         1.02         1.02 
TCGA-CG-5716 TCGA-CG-5717 TCGA-CG-5718 TCGA-CG-5719 TCGA-CG-5720 TCGA-CG-5721 
        1.02         6.94         1.02         1.02         0.99         5.98 
TCGA-CG-5722 TCGA-CG-5723 TCGA-CG-5724 TCGA-CG-5725 TCGA-CG-5726 TCGA-CG-5727 
        0.95        70.06        12.03        15.02        28.96        31.04 
TCGA-CG-5728 TCGA-CG-5730 TCGA-CG-5732 TCGA-CG-5733 TCGA-CG-5734 TCGA-D7-5577 
       65.10         4.01        55.04        21.07         7.99         8.65 
TCGA-D7-5578 TCGA-D7-6518 TCGA-D7-6519 TCGA-D7-6520 TCGA-D7-6521 TCGA-D7-6522 
        3.58         9.80        15.65         9.63         8.19         6.90 
TCGA-D7-6524 TCGA-D7-6525 TCGA-D7-6526 TCGA-D7-6527 TCGA-D7-6528 TCGA-D7-6815 
        0.69         5.95         6.61         4.14         1.68         3.65 
TCGA-D7-6817 TCGA-D7-6818 TCGA-D7-6820 TCGA-D7-6822 TCGA-EQ-5647 TCGA-EQ-8122 
        4.70         4.04         2.93         4.27         0.62         7.79 
TCGA-F1-6177 TCGA-F1-6874 TCGA-F1-6875 TCGA-FP-7735 TCGA-FP-7829 TCGA-FP-7916 
        6.54         2.01        72.23         0.39         0.20         3.02 
TCGA-FP-7998 TCGA-FP-8099 TCGA-FP-8209 TCGA-FP-8210 TCGA-FP-8631 TCGA-HJ-7597 
        3.58         1.02        59.05         5.03         0.56        26.43 
TCGA-IN-7806 TCGA-IN-7808 TCGA-IP-7968 
        6.87         3.55         2.53 

      4P GAIN CNV 4P GAIN WILD-TYPE 
             4.54              0.07 
      4P GAIN CNV 4P GAIN WILD-TYPE 
            29.98             72.23 
      4P GAIN CNV 4P GAIN WILD-TYPE 
            17.26              1.22 
[1] "4.5 - 30.0 (17.3)" "0.1 - 72.2 (1.2)" 
       TCGA-B7-5816        TCGA-B7-5818        TCGA-BR-6452        TCGA-BR-6455 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-BR-6457        TCGA-BR-6458        TCGA-BR-6563        TCGA-BR-6564 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-BR-6565        TCGA-BR-6566        TCGA-BR-6705        TCGA-BR-6706 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-BR-6707        TCGA-BR-6709        TCGA-BR-6710        TCGA-BR-6801 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-BR-6802        TCGA-BR-6803        TCGA-BR-6852        TCGA-BR-7196 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-BR-7197        TCGA-BR-7703        TCGA-BR-7704        TCGA-BR-7707 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-BR-7715        TCGA-BR-7716        TCGA-BR-7717        TCGA-BR-7722 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-BR-7723        TCGA-BR-7851        TCGA-BR-7901        TCGA-BR-7957 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-BR-7958        TCGA-BR-7959        TCGA-BR-8059        TCGA-BR-8060 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-BR-8077        TCGA-BR-8078        TCGA-BR-8080        TCGA-BR-8081 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-BR-8284        TCGA-BR-8285        TCGA-BR-8286        TCGA-BR-8289 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-BR-8291        TCGA-BR-8295        TCGA-BR-8296        TCGA-BR-8297 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-BR-8592        TCGA-BR-A4IU        TCGA-BR-A4IV        TCGA-BR-A4IY 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-BR-A4IZ        TCGA-BR-A4J1        TCGA-BR-A4J2        TCGA-BR-A4J4 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-BR-A4J5        TCGA-BR-A4J6        TCGA-BR-A4J8        TCGA-BR-A4J9 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-BR-A4PF        TCGA-BR-A4QI        TCGA-BR-A4QL        TCGA-CD-5798 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-CD-5799        TCGA-CD-5800        TCGA-CD-5801        TCGA-CD-5802 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-CD-5803        TCGA-CG-4300        TCGA-CG-4301        TCGA-CG-4304 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-CG-4305        TCGA-CG-4306        TCGA-CG-4436        TCGA-CG-4437 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-CG-4438        TCGA-CG-4440        TCGA-CG-4441        TCGA-CG-4443 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE"       "4P GAIN CNV" 
       TCGA-CG-4444        TCGA-CG-4449        TCGA-CG-4455        TCGA-CG-4460 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-CG-4462        TCGA-CG-4465        TCGA-CG-4466        TCGA-CG-4469 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-CG-4472        TCGA-CG-4474        TCGA-CG-4477        TCGA-CG-5716 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-CG-5717        TCGA-CG-5718        TCGA-CG-5719        TCGA-CG-5720 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-CG-5721        TCGA-CG-5722        TCGA-CG-5723        TCGA-CG-5724 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-CG-5725        TCGA-CG-5726        TCGA-CG-5727        TCGA-CG-5728 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-CG-5730        TCGA-CG-5732        TCGA-CG-5733        TCGA-CG-5734 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-D7-5577        TCGA-D7-5578        TCGA-D7-5579        TCGA-D7-6518 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE"       "4P GAIN CNV" "4P GAIN WILD-TYPE" 
       TCGA-D7-6519        TCGA-D7-6520        TCGA-D7-6521        TCGA-D7-6522 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-D7-6524        TCGA-D7-6525        TCGA-D7-6526        TCGA-D7-6527 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-D7-6528        TCGA-D7-6815        TCGA-D7-6817        TCGA-D7-6818 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-D7-6820        TCGA-D7-6822        TCGA-EQ-5647        TCGA-EQ-8122 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-F1-6177        TCGA-F1-6874        TCGA-F1-6875        TCGA-FP-7735 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-FP-7829        TCGA-FP-7916        TCGA-FP-7998        TCGA-FP-8099 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-FP-8209        TCGA-FP-8210        TCGA-FP-8631        TCGA-HJ-7597 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-IN-7806        TCGA-IN-7808        TCGA-IP-7968 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-B7-5816        TCGA-B7-5818        TCGA-BR-6452        TCGA-BR-6455 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-BR-6457        TCGA-BR-6458        TCGA-BR-6563        TCGA-BR-6564 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-BR-6565        TCGA-BR-6566        TCGA-BR-6705        TCGA-BR-6706 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-BR-6707        TCGA-BR-6709        TCGA-BR-6710        TCGA-BR-6801 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-BR-6802        TCGA-BR-6803        TCGA-BR-6852        TCGA-BR-7196 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-BR-7197        TCGA-BR-7703        TCGA-BR-7704        TCGA-BR-7707 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-BR-7715        TCGA-BR-7716        TCGA-BR-7717        TCGA-BR-7722 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-BR-7723        TCGA-BR-7851        TCGA-BR-7901        TCGA-BR-7957 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-BR-7958        TCGA-BR-7959        TCGA-BR-8059        TCGA-BR-8060 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-BR-8077        TCGA-BR-8078        TCGA-BR-8080        TCGA-BR-8081 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-BR-8284        TCGA-BR-8285        TCGA-BR-8286        TCGA-BR-8289 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-BR-8291        TCGA-BR-8295        TCGA-BR-8296        TCGA-BR-8297 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-BR-8592        TCGA-BR-A4IU        TCGA-BR-A4IV        TCGA-BR-A4IY 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-BR-A4IZ        TCGA-BR-A4J1        TCGA-BR-A4J2        TCGA-BR-A4J4 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-BR-A4J5        TCGA-BR-A4J6        TCGA-BR-A4J8        TCGA-BR-A4J9 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-BR-A4PF        TCGA-BR-A4QI        TCGA-BR-A4QL        TCGA-CD-5798 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-CD-5799        TCGA-CD-5800        TCGA-CD-5801        TCGA-CD-5802 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-CD-5803        TCGA-CG-4300        TCGA-CG-4301        TCGA-CG-4304 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-CG-4305        TCGA-CG-4306        TCGA-CG-4436        TCGA-CG-4437 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-CG-4438        TCGA-CG-4440        TCGA-CG-4441        TCGA-CG-4443 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE"       "4P GAIN CNV" 
       TCGA-CG-4444        TCGA-CG-4449        TCGA-CG-4455        TCGA-CG-4460 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-CG-4462        TCGA-CG-4465        TCGA-CG-4466        TCGA-CG-4469 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-CG-4472        TCGA-CG-4474        TCGA-CG-4477        TCGA-CG-5716 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-CG-5717        TCGA-CG-5718        TCGA-CG-5719        TCGA-CG-5720 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-CG-5721        TCGA-CG-5722        TCGA-CG-5723        TCGA-CG-5724 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-CG-5725        TCGA-CG-5726        TCGA-CG-5727        TCGA-CG-5728 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-CG-5730        TCGA-CG-5732        TCGA-CG-5733        TCGA-CG-5734 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-D7-5577        TCGA-D7-5578        TCGA-D7-5579        TCGA-D7-6518 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE"       "4P GAIN CNV" "4P GAIN WILD-TYPE" 
       TCGA-D7-6519        TCGA-D7-6520        TCGA-D7-6521        TCGA-D7-6522 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-D7-6524        TCGA-D7-6525        TCGA-D7-6526        TCGA-D7-6527 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-D7-6528        TCGA-D7-6815        TCGA-D7-6817        TCGA-D7-6818 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-D7-6820        TCGA-D7-6822        TCGA-EQ-5647        TCGA-EQ-8122 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-F1-6177        TCGA-F1-6874        TCGA-F1-6875        TCGA-FP-7735 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-FP-7829        TCGA-FP-7916        TCGA-FP-7998        TCGA-FP-8099 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-FP-8209        TCGA-FP-8210        TCGA-FP-8631        TCGA-HJ-7597 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-IN-7806        TCGA-IN-7808        TCGA-IP-7968 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-B7-5816        TCGA-B7-5818        TCGA-BR-6452        TCGA-BR-6455 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-BR-6457        TCGA-BR-6458        TCGA-BR-6563        TCGA-BR-6564 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-BR-6565        TCGA-BR-6566        TCGA-BR-6705        TCGA-BR-6706 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-BR-6707        TCGA-BR-6709        TCGA-BR-6710        TCGA-BR-6801 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-BR-6802        TCGA-BR-6803        TCGA-BR-6852        TCGA-BR-7196 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-BR-7197        TCGA-BR-7703        TCGA-BR-7704        TCGA-BR-7707 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-BR-7715        TCGA-BR-7716        TCGA-BR-7717        TCGA-BR-7722 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-BR-7723        TCGA-BR-7851        TCGA-BR-7901        TCGA-BR-7957 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-BR-7958        TCGA-BR-7959        TCGA-BR-8059        TCGA-BR-8060 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-BR-8077        TCGA-BR-8078        TCGA-BR-8080        TCGA-BR-8081 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-BR-8284        TCGA-BR-8285        TCGA-BR-8286        TCGA-BR-8289 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-BR-8291        TCGA-BR-8295        TCGA-BR-8296        TCGA-BR-8297 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-BR-8592        TCGA-BR-A4IU        TCGA-BR-A4IV        TCGA-BR-A4IY 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-BR-A4IZ        TCGA-BR-A4J1        TCGA-BR-A4J2        TCGA-BR-A4J4 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-BR-A4J5        TCGA-BR-A4J6        TCGA-BR-A4J8        TCGA-BR-A4J9 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-BR-A4PF        TCGA-BR-A4QI        TCGA-BR-A4QL        TCGA-CD-5798 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-CD-5799        TCGA-CD-5800        TCGA-CD-5801        TCGA-CD-5802 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-CD-5803        TCGA-CG-4300        TCGA-CG-4301        TCGA-CG-4304 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-CG-4305        TCGA-CG-4306        TCGA-CG-4436        TCGA-CG-4437 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-CG-4438        TCGA-CG-4440        TCGA-CG-4441        TCGA-CG-4443 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE"       "4P GAIN CNV" 
       TCGA-CG-4444        TCGA-CG-4449        TCGA-CG-4455        TCGA-CG-4460 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-CG-4462        TCGA-CG-4465        TCGA-CG-4466        TCGA-CG-4469 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-CG-4472        TCGA-CG-4474        TCGA-CG-4477        TCGA-CG-5716 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-CG-5717        TCGA-CG-5718        TCGA-CG-5719        TCGA-CG-5720 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-CG-5721        TCGA-CG-5722        TCGA-CG-5723        TCGA-CG-5724 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-CG-5725        TCGA-CG-5726        TCGA-CG-5727        TCGA-CG-5728 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-CG-5730        TCGA-CG-5732        TCGA-CG-5733        TCGA-CG-5734 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-D7-5577        TCGA-D7-5578        TCGA-D7-5579        TCGA-D7-6518 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE"       "4P GAIN CNV" "4P GAIN WILD-TYPE" 
       TCGA-D7-6519        TCGA-D7-6520        TCGA-D7-6521        TCGA-D7-6522 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-D7-6524        TCGA-D7-6525        TCGA-D7-6526        TCGA-D7-6527 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-D7-6528        TCGA-D7-6815        TCGA-D7-6817        TCGA-D7-6818 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-D7-6820        TCGA-D7-6822        TCGA-EQ-5647        TCGA-EQ-8122 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-F1-6177        TCGA-F1-6874        TCGA-F1-6875        TCGA-FP-7735 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-FP-7829        TCGA-FP-7916        TCGA-FP-7998        TCGA-FP-8099 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-FP-8209        TCGA-FP-8210        TCGA-FP-8631        TCGA-HJ-7597 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-IN-7806        TCGA-IN-7808        TCGA-IP-7968 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
[1] "Remove cluster labels:" "4P GAIN CNV"           
clus
      4P GAIN CNV 4P GAIN WILD-TYPE 
                2               141 
       TCGA-B7-5816        TCGA-B7-5818        TCGA-BR-6452        TCGA-BR-6455 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-BR-6457        TCGA-BR-6458        TCGA-BR-6563        TCGA-BR-6564 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-BR-6565        TCGA-BR-6566        TCGA-BR-6705        TCGA-BR-6706 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-BR-6707        TCGA-BR-6709        TCGA-BR-6710        TCGA-BR-6801 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-BR-6802        TCGA-BR-6803        TCGA-BR-6852        TCGA-BR-7196 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-BR-7197        TCGA-BR-7703        TCGA-BR-7704        TCGA-BR-7707 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-BR-7715        TCGA-BR-7716        TCGA-BR-7717        TCGA-BR-7722 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-BR-7723        TCGA-BR-7851        TCGA-BR-7901        TCGA-BR-7957 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-BR-7958        TCGA-BR-7959        TCGA-BR-8059        TCGA-BR-8060 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-BR-8077        TCGA-BR-8078        TCGA-BR-8080        TCGA-BR-8081 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-BR-8284        TCGA-BR-8285        TCGA-BR-8286        TCGA-BR-8289 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-BR-8291        TCGA-BR-8295        TCGA-BR-8296        TCGA-BR-8297 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-BR-8592        TCGA-BR-A4IU        TCGA-BR-A4IV        TCGA-BR-A4IY 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-BR-A4IZ        TCGA-BR-A4J1        TCGA-BR-A4J2        TCGA-BR-A4J4 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-BR-A4J5        TCGA-BR-A4J6        TCGA-BR-A4J8        TCGA-BR-A4J9 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-BR-A4PF        TCGA-BR-A4QI        TCGA-BR-A4QL        TCGA-CD-5798 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-CD-5799        TCGA-CD-5800        TCGA-CD-5801        TCGA-CD-5802 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-CD-5803        TCGA-CG-4300        TCGA-CG-4301        TCGA-CG-4304 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-CG-4305        TCGA-CG-4306        TCGA-CG-4436        TCGA-CG-4437 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-CG-4438        TCGA-CG-4440        TCGA-CG-4441        TCGA-CG-4444 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-CG-4449        TCGA-CG-4455        TCGA-CG-4460        TCGA-CG-4462 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-CG-4465        TCGA-CG-4466        TCGA-CG-4469        TCGA-CG-4472 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-CG-4474        TCGA-CG-4477        TCGA-CG-5716        TCGA-CG-5717 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-CG-5718        TCGA-CG-5719        TCGA-CG-5720        TCGA-CG-5721 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-CG-5722        TCGA-CG-5723        TCGA-CG-5724        TCGA-CG-5725 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-CG-5726        TCGA-CG-5727        TCGA-CG-5728        TCGA-CG-5730 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-CG-5732        TCGA-CG-5733        TCGA-CG-5734        TCGA-D7-5577 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-D7-5578        TCGA-D7-6518        TCGA-D7-6519        TCGA-D7-6520 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-D7-6521        TCGA-D7-6522        TCGA-D7-6524        TCGA-D7-6525 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-D7-6526        TCGA-D7-6527        TCGA-D7-6528        TCGA-D7-6815 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-D7-6817        TCGA-D7-6818        TCGA-D7-6820        TCGA-D7-6822 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-EQ-5647        TCGA-EQ-8122        TCGA-F1-6177        TCGA-F1-6874 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-F1-6875        TCGA-FP-7735        TCGA-FP-7829        TCGA-FP-7916 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-FP-7998        TCGA-FP-8099        TCGA-FP-8209        TCGA-FP-8210 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-FP-8631        TCGA-HJ-7597        TCGA-IN-7806        TCGA-IN-7808 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-IP-7968 
"4P GAIN WILD-TYPE" 
D7V2, continuous
D7V3, binary
[1] "tbl2"
                   cls
clus                [,1] [,2]
  4P GAIN CNV          0    3
  4P GAIN WILD-TYPE   72  105
        clus
vv       4P GAIN CNV 4P GAIN WILD-TYPE
  FEMALE           0                72
  MALE             3               105
                   vv
clus                STOMACH  ADENOCARCINOMA  DIFFUSE TYPE
  4P GAIN CNV                                           0
  4P GAIN WILD-TYPE                                    10
                   vv
clus                STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  4P GAIN CNV                                                            0
  4P GAIN WILD-TYPE                                                     16
                   vv
clus                STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  4P GAIN CNV                                                                       0
  4P GAIN WILD-TYPE                                                                 8
                   vv
clus                STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE
  4P GAIN CNV                                                              0
  4P GAIN WILD-TYPE                                                        3
                   vv
clus                STOMACH ADENOCARCINOMA  SIGNET RING TYPE
  4P GAIN CNV                                              0
  4P GAIN WILD-TYPE                                        1
                   vv
clus                STOMACH ADENOCARCINOMA - DIFFUSE TYPE
  4P GAIN CNV                                           0
  4P GAIN WILD-TYPE                                    16
                   vv
clus                STOMACH ADENOCARCINOMA - NOT OTHERWISE SPECIFIED (NOS)
  4P GAIN CNV                                                            0
  4P GAIN WILD-TYPE                                                     73
                   vv
clus                STOMACH INTESTINAL ADENOCARCINOMA - MUCINOUS TYPE
  4P GAIN CNV                                                       1
  4P GAIN WILD-TYPE                                                 6
                   vv
clus                STOMACH INTESTINAL ADENOCARCINOMA - PAPILLARY TYPE
  4P GAIN CNV                                                        0
  4P GAIN WILD-TYPE                                                  3
                   vv
clus                STOMACH INTESTINAL ADENOCARCINOMA - TUBULAR TYPE
  4P GAIN CNV                                                      0
  4P GAIN WILD-TYPE                                               10
                   vv
clus                STOMACH INTESTINAL ADENOCARCINOMA - TYPE NOT OTHERWISE SPECIFIED (NOS)
  4P GAIN CNV                                                                            1
  4P GAIN WILD-TYPE                                                                     27
D7V4, multiclass
[1] "Remove cluster labels:" "4P GAIN CNV"           
clus
      4P GAIN CNV 4P GAIN WILD-TYPE 
                2               173 
       TCGA-B7-5816        TCGA-B7-5818        TCGA-BR-4183        TCGA-BR-4184 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-BR-4187        TCGA-BR-4188        TCGA-BR-4191        TCGA-BR-4201 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-BR-4253        TCGA-BR-4255        TCGA-BR-4256        TCGA-BR-4257 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-BR-4267        TCGA-BR-4279        TCGA-BR-4280        TCGA-BR-4292 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-BR-4294        TCGA-BR-4357        TCGA-BR-4361        TCGA-BR-4362 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-BR-4363        TCGA-BR-4366        TCGA-BR-4367        TCGA-BR-4368 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-BR-4369        TCGA-BR-4370        TCGA-BR-4371        TCGA-BR-6452 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-BR-6453        TCGA-BR-6454        TCGA-BR-6455        TCGA-BR-6456 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-BR-6457        TCGA-BR-6458        TCGA-BR-6563        TCGA-BR-6564 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-BR-6565        TCGA-BR-6566        TCGA-BR-6705        TCGA-BR-6706 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-BR-6707        TCGA-BR-6709        TCGA-BR-6710        TCGA-BR-6801 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-BR-6802        TCGA-BR-6803        TCGA-BR-6852        TCGA-BR-7196 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-BR-7197        TCGA-BR-7703        TCGA-BR-7704        TCGA-BR-7707 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-BR-7715        TCGA-BR-7716        TCGA-BR-7717        TCGA-BR-7722 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-BR-7723        TCGA-BR-7851        TCGA-BR-7901        TCGA-BR-7957 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-BR-7958        TCGA-BR-7959        TCGA-BR-8059        TCGA-BR-8060 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-BR-8077        TCGA-BR-8078        TCGA-BR-8080        TCGA-BR-8081 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-BR-8284        TCGA-BR-8285        TCGA-BR-8286        TCGA-BR-8289 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-BR-8291        TCGA-BR-8295        TCGA-BR-8296        TCGA-BR-8297 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-BR-8592        TCGA-BR-A4IU        TCGA-BR-A4IV        TCGA-BR-A4IY 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-BR-A4IZ        TCGA-BR-A4J1        TCGA-BR-A4J2        TCGA-BR-A4J4 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-BR-A4J5        TCGA-BR-A4J6        TCGA-BR-A4J8        TCGA-BR-A4J9 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-BR-A4PF        TCGA-BR-A4QI        TCGA-BR-A4QL        TCGA-CD-5798 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-CD-5799        TCGA-CD-5800        TCGA-CD-5801        TCGA-CD-5802 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-CD-5803        TCGA-CD-5804        TCGA-CG-4300        TCGA-CG-4301 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-CG-4304        TCGA-CG-4305        TCGA-CG-4306        TCGA-CG-4436 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-CG-4437        TCGA-CG-4438        TCGA-CG-4440        TCGA-CG-4441 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-CG-4442        TCGA-CG-4449        TCGA-CG-4455        TCGA-CG-4460 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-CG-4466        TCGA-CG-4469        TCGA-CG-4474        TCGA-CG-4476 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-CG-4477        TCGA-CG-5716        TCGA-CG-5717        TCGA-CG-5718 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-CG-5719        TCGA-CG-5720        TCGA-CG-5721        TCGA-CG-5722 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-CG-5723        TCGA-CG-5724        TCGA-CG-5725        TCGA-CG-5726 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-CG-5727        TCGA-CG-5728        TCGA-CG-5730        TCGA-CG-5732 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-CG-5733        TCGA-CG-5734        TCGA-D7-5577        TCGA-D7-5578 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-D7-6518        TCGA-D7-6519        TCGA-D7-6520        TCGA-D7-6521 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-D7-6522        TCGA-D7-6524        TCGA-D7-6525        TCGA-D7-6526 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-D7-6527        TCGA-D7-6528        TCGA-D7-6815        TCGA-D7-6817 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-D7-6818        TCGA-D7-6820        TCGA-D7-6822        TCGA-EQ-5647 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-EQ-8122        TCGA-F1-6177        TCGA-F1-6874        TCGA-F1-6875 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-FP-7735        TCGA-FP-7829        TCGA-FP-7916        TCGA-FP-7998 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-FP-8099        TCGA-FP-8209        TCGA-FP-8210        TCGA-FP-8631 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-HF-7131        TCGA-HF-7132        TCGA-HF-7133        TCGA-HF-7134 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-HF-7136        TCGA-HJ-7597        TCGA-IN-7806        TCGA-IN-7808 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-IP-7968 
"4P GAIN WILD-TYPE" 
                   vv
clus                T1 T2 T3 T4
  4P GAIN CNV        1  0  2  0
  4P GAIN WILD-TYPE  5 52 54 18
D7V5, multiclass
    clus
vv   4P GAIN CNV 4P GAIN WILD-TYPE
  T1           1                 5
  T2           0                52
  T3           2                54
  T4           0                18
                   vv
clus                N0 N1 N2 N3
  4P GAIN CNV        1  1  1  0
  4P GAIN WILD-TYPE 43 48 22 15
D7V6, multiclass
    clus
vv   4P GAIN CNV 4P GAIN WILD-TYPE
  N0           1                43
  N1           1                48
  N2           1                22
  N3           0                15
                   vv
clus                 M0  M1  MX
  4P GAIN CNV         3   0   0
  4P GAIN WILD-TYPE 115  16   8
D7V7, multiclass
    clus
vv   4P GAIN CNV 4P GAIN WILD-TYPE
  M0           3               115
  M1           0                16
  MX           0                 8
                   vv
clus                 I II III IV
  4P GAIN CNV        1  2   0  0
  4P GAIN WILD-TYPE 23 35  39 26
D7V8, multiclass
     clus
vv    4P GAIN CNV 4P GAIN WILD-TYPE
  I             1                23
  II            2                35
  III           0                39
  IV            0                26
D7V9, binary
[1] "tbl2"
                   cls
clus                [,1] [,2]
  4P GAIN CNV          0    3
  4P GAIN WILD-TYPE    5  172
     clus
vv    4P GAIN CNV 4P GAIN WILD-TYPE
  NO            0                 5
  YES           3               172
                   vv
clus                 R0  R1  R2  RX
  4P GAIN CNV         2   1   0   0
  4P GAIN WILD-TYPE 123   6  12  25
D7V10, multiclass
    clus
vv   4P GAIN CNV 4P GAIN WILD-TYPE
  R0           2               123
  R1           1                 6
  R2           0                12
  RX           0                25
D7V11, continuous
[1] "Remove cluster labels:" "4P GAIN CNV"           
clus
      4P GAIN CNV 4P GAIN WILD-TYPE 
                1               135 
       TCGA-B7-5816        TCGA-BR-4183        TCGA-BR-4184        TCGA-BR-4188 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-BR-4191        TCGA-BR-4253        TCGA-BR-4255        TCGA-BR-4256 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-BR-4267        TCGA-BR-4279        TCGA-BR-4280        TCGA-BR-4361 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-BR-4362        TCGA-BR-4367        TCGA-BR-4368        TCGA-BR-6452 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-BR-6453        TCGA-BR-6454        TCGA-BR-6455        TCGA-BR-6456 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-BR-6457        TCGA-BR-6458        TCGA-BR-6563        TCGA-BR-6564 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-BR-6565        TCGA-BR-6566        TCGA-BR-6705        TCGA-BR-6706 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-BR-6707        TCGA-BR-6709        TCGA-BR-6710        TCGA-BR-6801 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-BR-6802        TCGA-BR-6803        TCGA-BR-6852        TCGA-BR-7196 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-BR-7197        TCGA-BR-7703        TCGA-BR-7704        TCGA-BR-7707 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-BR-7715        TCGA-BR-7716        TCGA-BR-7717        TCGA-BR-7722 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-BR-7723        TCGA-BR-7851        TCGA-BR-7901        TCGA-BR-7957 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-BR-7958        TCGA-BR-7959        TCGA-BR-8059        TCGA-BR-8060 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-BR-8077        TCGA-BR-8078        TCGA-BR-8080        TCGA-BR-8081 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-BR-8284        TCGA-BR-8285        TCGA-BR-8286        TCGA-BR-8289 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-BR-8291        TCGA-BR-8295        TCGA-BR-8296        TCGA-BR-8297 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-BR-8592        TCGA-BR-A4IU        TCGA-BR-A4IV        TCGA-BR-A4IY 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-BR-A4IZ        TCGA-BR-A4J1        TCGA-BR-A4J2        TCGA-BR-A4J4 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-BR-A4J5        TCGA-BR-A4J6        TCGA-BR-A4J8        TCGA-BR-A4J9 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-BR-A4PF        TCGA-BR-A4QI        TCGA-BR-A4QL        TCGA-CD-5804 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-CG-5717        TCGA-CG-5718        TCGA-CG-5719        TCGA-CG-5720 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-CG-5721        TCGA-CG-5722        TCGA-CG-5723        TCGA-CG-5724 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-CG-5725        TCGA-CG-5726        TCGA-CG-5727        TCGA-CG-5728 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-CG-5730        TCGA-CG-5732        TCGA-CG-5733        TCGA-CG-5734 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-D7-5577        TCGA-D7-5578        TCGA-D7-6518        TCGA-D7-6519 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-D7-6520        TCGA-D7-6521        TCGA-D7-6522        TCGA-D7-6524 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-D7-6525        TCGA-D7-6526        TCGA-D7-6527        TCGA-D7-6528 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-D7-6815        TCGA-D7-6817        TCGA-D7-6818        TCGA-D7-6820 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-D7-6822        TCGA-EQ-5647        TCGA-EQ-8122        TCGA-F1-6177 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-F1-6874        TCGA-F1-6875        TCGA-FP-7735        TCGA-FP-7829 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-FP-7916        TCGA-FP-7998        TCGA-FP-8099        TCGA-FP-8209 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-FP-8210        TCGA-FP-8631        TCGA-HF-7131        TCGA-HF-7132 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-HF-7133        TCGA-HF-7134        TCGA-HF-7136        TCGA-HJ-7597 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-IN-7806        TCGA-IN-7808        TCGA-IP-7968 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 

Clustering(8) Variable = 5p gain
D8V1, survival
                   sevent
clus2                 0   1
  5P GAIN CNV        20   4
  5P GAIN WILD-TYPE 104  15
      5P GAIN CNV 5P GAIN WILD-TYPE 
               24               119 
      5P GAIN CNV 5P GAIN WILD-TYPE 
                4                15 
$`5P GAIN CNV`
TCGA-BR-7197 TCGA-BR-7704 TCGA-BR-7715 TCGA-BR-7717 TCGA-BR-8060 TCGA-BR-8077 
        1.48         1.25         1.05         0.69         1.32         0.69 
TCGA-BR-8284 TCGA-CD-5801 TCGA-CG-4436 TCGA-CG-4438 TCGA-CG-4444 TCGA-CG-4455 
        0.72         0.49        52.96        54.05        47.05        12.03 
TCGA-CG-4460 TCGA-CG-4466 TCGA-CG-4472 TCGA-CG-5718 TCGA-CG-5722 TCGA-CG-5724 
       21.99        18.94        12.00         1.02         0.95        12.03 
TCGA-CG-5725 TCGA-D7-5579 TCGA-D7-6818 TCGA-D7-6820 TCGA-EQ-5647 TCGA-FP-7829 
       15.02         4.54         4.04         2.93         0.62         0.20 

$`5P GAIN WILD-TYPE`
TCGA-B7-5816 TCGA-B7-5818 TCGA-BR-6452 TCGA-BR-6455 TCGA-BR-6457 TCGA-BR-6458 
        5.62         0.10         0.95         1.41         1.35         1.35 
TCGA-BR-6563 TCGA-BR-6564 TCGA-BR-6565 TCGA-BR-6566 TCGA-BR-6705 TCGA-BR-6706 
        0.85         0.82         0.62         0.62         1.71         2.17 
TCGA-BR-6707 TCGA-BR-6709 TCGA-BR-6710 TCGA-BR-6801 TCGA-BR-6802 TCGA-BR-6803 
        0.99         1.22         0.66         1.12         0.76         0.66 
TCGA-BR-6852 TCGA-BR-7196 TCGA-BR-7703 TCGA-BR-7707 TCGA-BR-7716 TCGA-BR-7722 
        0.26         1.22         0.46         0.13         0.82         0.16 
TCGA-BR-7723 TCGA-BR-7851 TCGA-BR-7901 TCGA-BR-7957 TCGA-BR-7958 TCGA-BR-7959 
        4.54         0.99         0.95         0.69         0.16         1.08 
TCGA-BR-8059 TCGA-BR-8078 TCGA-BR-8080 TCGA-BR-8081 TCGA-BR-8285 TCGA-BR-8286 
        0.82         0.95         0.49         0.46         0.26         0.43 
TCGA-BR-8289 TCGA-BR-8291 TCGA-BR-8295 TCGA-BR-8296 TCGA-BR-8297 TCGA-BR-8592 
        0.26         1.18         1.55         1.48         0.76         0.20 
TCGA-BR-A4IU TCGA-BR-A4IV TCGA-BR-A4IY TCGA-BR-A4IZ TCGA-BR-A4J1 TCGA-BR-A4J2 
        0.59         0.92         0.39         0.79         0.72         0.79 
TCGA-BR-A4J4 TCGA-BR-A4J5 TCGA-BR-A4J6 TCGA-BR-A4J8 TCGA-BR-A4J9 TCGA-BR-A4PF 
        0.53         0.43         0.13         0.23         0.10         0.72 
TCGA-BR-A4QI TCGA-BR-A4QL TCGA-CD-5798 TCGA-CD-5799 TCGA-CD-5800 TCGA-CD-5802 
        0.49         2.24         0.82         0.69         0.36         0.30 
TCGA-CD-5803 TCGA-CG-4300 TCGA-CG-4301 TCGA-CG-4304 TCGA-CG-4305 TCGA-CG-4306 
        0.07        20.02         3.02        27.02        15.95         1.02 
TCGA-CG-4437 TCGA-CG-4440 TCGA-CG-4441 TCGA-CG-4443 TCGA-CG-4449 TCGA-CG-4462 
        8.05         4.01        14.01        29.98        19.07         1.02 
TCGA-CG-4465 TCGA-CG-4469 TCGA-CG-4474 TCGA-CG-4477 TCGA-CG-5716 TCGA-CG-5717 
        8.98         7.07         1.02         1.02         1.02         6.94 
TCGA-CG-5719 TCGA-CG-5720 TCGA-CG-5721 TCGA-CG-5723 TCGA-CG-5726 TCGA-CG-5727 
        1.02         0.99         5.98        70.06        28.96        31.04 
TCGA-CG-5728 TCGA-CG-5730 TCGA-CG-5732 TCGA-CG-5733 TCGA-CG-5734 TCGA-D7-5577 
       65.10         4.01        55.04        21.07         7.99         8.65 
TCGA-D7-5578 TCGA-D7-6518 TCGA-D7-6519 TCGA-D7-6520 TCGA-D7-6521 TCGA-D7-6522 
        3.58         9.80        15.65         9.63         8.19         6.90 
TCGA-D7-6524 TCGA-D7-6525 TCGA-D7-6526 TCGA-D7-6527 TCGA-D7-6528 TCGA-D7-6815 
        0.69         5.95         6.61         4.14         1.68         3.65 
TCGA-D7-6817 TCGA-D7-6822 TCGA-EQ-8122 TCGA-F1-6177 TCGA-F1-6874 TCGA-F1-6875 
        4.70         4.27         7.79         6.54         2.01        72.23 
TCGA-FP-7735 TCGA-FP-7916 TCGA-FP-7998 TCGA-FP-8099 TCGA-FP-8209 TCGA-FP-8210 
        0.39         3.02         3.58         1.02        59.05         5.03 
TCGA-FP-8631 TCGA-HJ-7597 TCGA-IN-7806 TCGA-IN-7808 TCGA-IP-7968 
        0.56        26.43         6.87         3.55         2.53 

      5P GAIN CNV 5P GAIN WILD-TYPE 
             0.20              0.07 
      5P GAIN CNV 5P GAIN WILD-TYPE 
            54.05             72.23 
      5P GAIN CNV 5P GAIN WILD-TYPE 
            2.205             1.180 
[1] "0.2 - 54.0 (2.2)" "0.1 - 72.2 (1.2)"
       TCGA-B7-5816        TCGA-B7-5818        TCGA-BR-6452        TCGA-BR-6455 
"5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" 
       TCGA-BR-6457        TCGA-BR-6458        TCGA-BR-6563        TCGA-BR-6564 
"5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" 
       TCGA-BR-6565        TCGA-BR-6566        TCGA-BR-6705        TCGA-BR-6706 
"5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" 
       TCGA-BR-6707        TCGA-BR-6709        TCGA-BR-6710        TCGA-BR-6801 
"5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" 
       TCGA-BR-6802        TCGA-BR-6803        TCGA-BR-6852        TCGA-BR-7196 
"5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" 
       TCGA-BR-7197        TCGA-BR-7703        TCGA-BR-7704        TCGA-BR-7707 
      "5P GAIN CNV" "5P GAIN WILD-TYPE"       "5P GAIN CNV" "5P GAIN WILD-TYPE" 
       TCGA-BR-7715        TCGA-BR-7716        TCGA-BR-7717        TCGA-BR-7722 
      "5P GAIN CNV" "5P GAIN WILD-TYPE"       "5P GAIN CNV" "5P GAIN WILD-TYPE" 
       TCGA-BR-7723        TCGA-BR-7851        TCGA-BR-7901        TCGA-BR-7957 
"5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" 
       TCGA-BR-7958        TCGA-BR-7959        TCGA-BR-8059        TCGA-BR-8060 
"5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE"       "5P GAIN CNV" 
       TCGA-BR-8077        TCGA-BR-8078        TCGA-BR-8080        TCGA-BR-8081 
      "5P GAIN CNV" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" 
       TCGA-BR-8284        TCGA-BR-8285        TCGA-BR-8286        TCGA-BR-8289 
      "5P GAIN CNV" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" 
       TCGA-BR-8291        TCGA-BR-8295        TCGA-BR-8296        TCGA-BR-8297 
"5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" 
       TCGA-BR-8592        TCGA-BR-A4IU        TCGA-BR-A4IV        TCGA-BR-A4IY 
"5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" 
       TCGA-BR-A4IZ        TCGA-BR-A4J1        TCGA-BR-A4J2        TCGA-BR-A4J4 
"5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" 
       TCGA-BR-A4J5        TCGA-BR-A4J6        TCGA-BR-A4J8        TCGA-BR-A4J9 
"5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" 
       TCGA-BR-A4PF        TCGA-BR-A4QI        TCGA-BR-A4QL        TCGA-CD-5798 
"5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" 
       TCGA-CD-5799        TCGA-CD-5800        TCGA-CD-5801        TCGA-CD-5802 
"5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE"       "5P GAIN CNV" "5P GAIN WILD-TYPE" 
       TCGA-CD-5803        TCGA-CG-4300        TCGA-CG-4301        TCGA-CG-4304 
"5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" 
       TCGA-CG-4305        TCGA-CG-4306        TCGA-CG-4436        TCGA-CG-4437 
"5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE"       "5P GAIN CNV" "5P GAIN WILD-TYPE" 
       TCGA-CG-4438        TCGA-CG-4440        TCGA-CG-4441        TCGA-CG-4443 
      "5P GAIN CNV" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" 
       TCGA-CG-4444        TCGA-CG-4449        TCGA-CG-4455        TCGA-CG-4460 
      "5P GAIN CNV" "5P GAIN WILD-TYPE"       "5P GAIN CNV"       "5P GAIN CNV" 
       TCGA-CG-4462        TCGA-CG-4465        TCGA-CG-4466        TCGA-CG-4469 
"5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE"       "5P GAIN CNV" "5P GAIN WILD-TYPE" 
       TCGA-CG-4472        TCGA-CG-4474        TCGA-CG-4477        TCGA-CG-5716 
      "5P GAIN CNV" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" 
       TCGA-CG-5717        TCGA-CG-5718        TCGA-CG-5719        TCGA-CG-5720 
"5P GAIN WILD-TYPE"       "5P GAIN CNV" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" 
       TCGA-CG-5721        TCGA-CG-5722        TCGA-CG-5723        TCGA-CG-5724 
"5P GAIN WILD-TYPE"       "5P GAIN CNV" "5P GAIN WILD-TYPE"       "5P GAIN CNV" 
       TCGA-CG-5725        TCGA-CG-5726        TCGA-CG-5727        TCGA-CG-5728 
      "5P GAIN CNV" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" 
       TCGA-CG-5730        TCGA-CG-5732        TCGA-CG-5733        TCGA-CG-5734 
"5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" 
       TCGA-D7-5577        TCGA-D7-5578        TCGA-D7-5579        TCGA-D7-6518 
"5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE"       "5P GAIN CNV" "5P GAIN WILD-TYPE" 
       TCGA-D7-6519        TCGA-D7-6520        TCGA-D7-6521        TCGA-D7-6522 
"5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" 
       TCGA-D7-6524        TCGA-D7-6525        TCGA-D7-6526        TCGA-D7-6527 
"5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" 
       TCGA-D7-6528        TCGA-D7-6815        TCGA-D7-6817        TCGA-D7-6818 
"5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE"       "5P GAIN CNV" 
       TCGA-D7-6820        TCGA-D7-6822        TCGA-EQ-5647        TCGA-EQ-8122 
      "5P GAIN CNV" "5P GAIN WILD-TYPE"       "5P GAIN CNV" "5P GAIN WILD-TYPE" 
       TCGA-F1-6177        TCGA-F1-6874        TCGA-F1-6875        TCGA-FP-7735 
"5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" 
       TCGA-FP-7829        TCGA-FP-7916        TCGA-FP-7998        TCGA-FP-8099 
      "5P GAIN CNV" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" 
       TCGA-FP-8209        TCGA-FP-8210        TCGA-FP-8631        TCGA-HJ-7597 
"5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" 
       TCGA-IN-7806        TCGA-IN-7808        TCGA-IP-7968 
"5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" 
       TCGA-B7-5816        TCGA-B7-5818        TCGA-BR-6452        TCGA-BR-6455 
"5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" 
       TCGA-BR-6457        TCGA-BR-6458        TCGA-BR-6563        TCGA-BR-6564 
"5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" 
       TCGA-BR-6565        TCGA-BR-6566        TCGA-BR-6705        TCGA-BR-6706 
"5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" 
       TCGA-BR-6707        TCGA-BR-6709        TCGA-BR-6710        TCGA-BR-6801 
"5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" 
       TCGA-BR-6802        TCGA-BR-6803        TCGA-BR-6852        TCGA-BR-7196 
"5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" 
       TCGA-BR-7197        TCGA-BR-7703        TCGA-BR-7704        TCGA-BR-7707 
      "5P GAIN CNV" "5P GAIN WILD-TYPE"       "5P GAIN CNV" "5P GAIN WILD-TYPE" 
       TCGA-BR-7715        TCGA-BR-7716        TCGA-BR-7717        TCGA-BR-7722 
      "5P GAIN CNV" "5P GAIN WILD-TYPE"       "5P GAIN CNV" "5P GAIN WILD-TYPE" 
       TCGA-BR-7723        TCGA-BR-7851        TCGA-BR-7901        TCGA-BR-7957 
"5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" 
       TCGA-BR-7958        TCGA-BR-7959        TCGA-BR-8059        TCGA-BR-8060 
"5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE"       "5P GAIN CNV" 
       TCGA-BR-8077        TCGA-BR-8078        TCGA-BR-8080        TCGA-BR-8081 
      "5P GAIN CNV" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" 
       TCGA-BR-8284        TCGA-BR-8285        TCGA-BR-8286        TCGA-BR-8289 
      "5P GAIN CNV" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" 
       TCGA-BR-8291        TCGA-BR-8295        TCGA-BR-8296        TCGA-BR-8297 
"5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" 
       TCGA-BR-8592        TCGA-BR-A4IU        TCGA-BR-A4IV        TCGA-BR-A4IY 
"5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" 
       TCGA-BR-A4IZ        TCGA-BR-A4J1        TCGA-BR-A4J2        TCGA-BR-A4J4 
"5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" 
       TCGA-BR-A4J5        TCGA-BR-A4J6        TCGA-BR-A4J8        TCGA-BR-A4J9 
"5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" 
       TCGA-BR-A4PF        TCGA-BR-A4QI        TCGA-BR-A4QL        TCGA-CD-5798 
"5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" 
       TCGA-CD-5799        TCGA-CD-5800        TCGA-CD-5801        TCGA-CD-5802 
"5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE"       "5P GAIN CNV" "5P GAIN WILD-TYPE" 
       TCGA-CD-5803        TCGA-CG-4300        TCGA-CG-4301        TCGA-CG-4304 
"5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" 
       TCGA-CG-4305        TCGA-CG-4306        TCGA-CG-4436        TCGA-CG-4437 
"5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE"       "5P GAIN CNV" "5P GAIN WILD-TYPE" 
       TCGA-CG-4438        TCGA-CG-4440        TCGA-CG-4441        TCGA-CG-4443 
      "5P GAIN CNV" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" 
       TCGA-CG-4444        TCGA-CG-4449        TCGA-CG-4455        TCGA-CG-4460 
      "5P GAIN CNV" "5P GAIN WILD-TYPE"       "5P GAIN CNV"       "5P GAIN CNV" 
       TCGA-CG-4462        TCGA-CG-4465        TCGA-CG-4466        TCGA-CG-4469 
"5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE"       "5P GAIN CNV" "5P GAIN WILD-TYPE" 
       TCGA-CG-4472        TCGA-CG-4474        TCGA-CG-4477        TCGA-CG-5716 
      "5P GAIN CNV" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" 
       TCGA-CG-5717        TCGA-CG-5718        TCGA-CG-5719        TCGA-CG-5720 
"5P GAIN WILD-TYPE"       "5P GAIN CNV" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" 
       TCGA-CG-5721        TCGA-CG-5722        TCGA-CG-5723        TCGA-CG-5724 
"5P GAIN WILD-TYPE"       "5P GAIN CNV" "5P GAIN WILD-TYPE"       "5P GAIN CNV" 
       TCGA-CG-5725        TCGA-CG-5726        TCGA-CG-5727        TCGA-CG-5728 
      "5P GAIN CNV" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" 
       TCGA-CG-5730        TCGA-CG-5732        TCGA-CG-5733        TCGA-CG-5734 
"5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" 
       TCGA-D7-5577        TCGA-D7-5578        TCGA-D7-5579        TCGA-D7-6518 
"5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE"       "5P GAIN CNV" "5P GAIN WILD-TYPE" 
       TCGA-D7-6519        TCGA-D7-6520        TCGA-D7-6521        TCGA-D7-6522 
"5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" 
       TCGA-D7-6524        TCGA-D7-6525        TCGA-D7-6526        TCGA-D7-6527 
"5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" 
       TCGA-D7-6528        TCGA-D7-6815        TCGA-D7-6817        TCGA-D7-6818 
"5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE"       "5P GAIN CNV" 
       TCGA-D7-6820        TCGA-D7-6822        TCGA-EQ-5647        TCGA-EQ-8122 
      "5P GAIN CNV" "5P GAIN WILD-TYPE"       "5P GAIN CNV" "5P GAIN WILD-TYPE" 
       TCGA-F1-6177        TCGA-F1-6874        TCGA-F1-6875        TCGA-FP-7735 
"5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" 
       TCGA-FP-7829        TCGA-FP-7916        TCGA-FP-7998        TCGA-FP-8099 
      "5P GAIN CNV" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" 
       TCGA-FP-8209        TCGA-FP-8210        TCGA-FP-8631        TCGA-HJ-7597 
"5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" 
       TCGA-IN-7806        TCGA-IN-7808        TCGA-IP-7968 
"5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" 
       TCGA-B7-5816        TCGA-B7-5818        TCGA-BR-6452        TCGA-BR-6455 
"5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" 
       TCGA-BR-6457        TCGA-BR-6458        TCGA-BR-6563        TCGA-BR-6564 
"5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" 
       TCGA-BR-6565        TCGA-BR-6566        TCGA-BR-6705        TCGA-BR-6706 
"5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" 
       TCGA-BR-6707        TCGA-BR-6709        TCGA-BR-6710        TCGA-BR-6801 
"5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" 
       TCGA-BR-6802        TCGA-BR-6803        TCGA-BR-6852        TCGA-BR-7196 
"5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" 
       TCGA-BR-7197        TCGA-BR-7703        TCGA-BR-7704        TCGA-BR-7707 
      "5P GAIN CNV" "5P GAIN WILD-TYPE"       "5P GAIN CNV" "5P GAIN WILD-TYPE" 
       TCGA-BR-7715        TCGA-BR-7716        TCGA-BR-7717        TCGA-BR-7722 
      "5P GAIN CNV" "5P GAIN WILD-TYPE"       "5P GAIN CNV" "5P GAIN WILD-TYPE" 
       TCGA-BR-7723        TCGA-BR-7851        TCGA-BR-7901        TCGA-BR-7957 
"5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" 
       TCGA-BR-7958        TCGA-BR-7959        TCGA-BR-8059        TCGA-BR-8060 
"5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE"       "5P GAIN CNV" 
       TCGA-BR-8077        TCGA-BR-8078        TCGA-BR-8080        TCGA-BR-8081 
      "5P GAIN CNV" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" 
       TCGA-BR-8284        TCGA-BR-8285        TCGA-BR-8286        TCGA-BR-8289 
      "5P GAIN CNV" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" 
       TCGA-BR-8291        TCGA-BR-8295        TCGA-BR-8296        TCGA-BR-8297 
"5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" 
       TCGA-BR-8592        TCGA-BR-A4IU        TCGA-BR-A4IV        TCGA-BR-A4IY 
"5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" 
       TCGA-BR-A4IZ        TCGA-BR-A4J1        TCGA-BR-A4J2        TCGA-BR-A4J4 
"5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" 
       TCGA-BR-A4J5        TCGA-BR-A4J6        TCGA-BR-A4J8        TCGA-BR-A4J9 
"5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" 
       TCGA-BR-A4PF        TCGA-BR-A4QI        TCGA-BR-A4QL        TCGA-CD-5798 
"5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" 
       TCGA-CD-5799        TCGA-CD-5800        TCGA-CD-5801        TCGA-CD-5802 
"5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE"       "5P GAIN CNV" "5P GAIN WILD-TYPE" 
       TCGA-CD-5803        TCGA-CG-4300        TCGA-CG-4301        TCGA-CG-4304 
"5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" 
       TCGA-CG-4305        TCGA-CG-4306        TCGA-CG-4436        TCGA-CG-4437 
"5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE"       "5P GAIN CNV" "5P GAIN WILD-TYPE" 
       TCGA-CG-4438        TCGA-CG-4440        TCGA-CG-4441        TCGA-CG-4443 
      "5P GAIN CNV" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" 
       TCGA-CG-4444        TCGA-CG-4449        TCGA-CG-4455        TCGA-CG-4460 
      "5P GAIN CNV" "5P GAIN WILD-TYPE"       "5P GAIN CNV"       "5P GAIN CNV" 
       TCGA-CG-4462        TCGA-CG-4465        TCGA-CG-4466        TCGA-CG-4469 
"5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE"       "5P GAIN CNV" "5P GAIN WILD-TYPE" 
       TCGA-CG-4472        TCGA-CG-4474        TCGA-CG-4477        TCGA-CG-5716 
      "5P GAIN CNV" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" 
       TCGA-CG-5717        TCGA-CG-5718        TCGA-CG-5719        TCGA-CG-5720 
"5P GAIN WILD-TYPE"       "5P GAIN CNV" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" 
       TCGA-CG-5721        TCGA-CG-5722        TCGA-CG-5723        TCGA-CG-5724 
"5P GAIN WILD-TYPE"       "5P GAIN CNV" "5P GAIN WILD-TYPE"       "5P GAIN CNV" 
       TCGA-CG-5725        TCGA-CG-5726        TCGA-CG-5727        TCGA-CG-5728 
      "5P GAIN CNV" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" 
       TCGA-CG-5730        TCGA-CG-5732        TCGA-CG-5733        TCGA-CG-5734 
"5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" 
       TCGA-D7-5577        TCGA-D7-5578        TCGA-D7-5579        TCGA-D7-6518 
"5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE"       "5P GAIN CNV" "5P GAIN WILD-TYPE" 
       TCGA-D7-6519        TCGA-D7-6520        TCGA-D7-6521        TCGA-D7-6522 
"5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" 
       TCGA-D7-6524        TCGA-D7-6525        TCGA-D7-6526        TCGA-D7-6527 
"5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" 
       TCGA-D7-6528        TCGA-D7-6815        TCGA-D7-6817        TCGA-D7-6818 
"5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE"       "5P GAIN CNV" 
       TCGA-D7-6820        TCGA-D7-6822        TCGA-EQ-5647        TCGA-EQ-8122 
      "5P GAIN CNV" "5P GAIN WILD-TYPE"       "5P GAIN CNV" "5P GAIN WILD-TYPE" 
       TCGA-F1-6177        TCGA-F1-6874        TCGA-F1-6875        TCGA-FP-7735 
"5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" 
       TCGA-FP-7829        TCGA-FP-7916        TCGA-FP-7998        TCGA-FP-8099 
      "5P GAIN CNV" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" 
       TCGA-FP-8209        TCGA-FP-8210        TCGA-FP-8631        TCGA-HJ-7597 
"5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" 
       TCGA-IN-7806        TCGA-IN-7808        TCGA-IP-7968 
"5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" 
[1] "hr=" "1.1"
D8V2, continuous
D8V3, binary
[1] "tbl2"
                   cls
clus                [,1] [,2]
  5P GAIN CNV         10   18
  5P GAIN WILD-TYPE   62   90
        clus
vv       5P GAIN CNV 5P GAIN WILD-TYPE
  FEMALE          10                62
  MALE            18                90
                   vv
clus                STOMACH  ADENOCARCINOMA  DIFFUSE TYPE
  5P GAIN CNV                                           0
  5P GAIN WILD-TYPE                                    10
                   vv
clus                STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  5P GAIN CNV                                                            1
  5P GAIN WILD-TYPE                                                     15
                   vv
clus                STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  5P GAIN CNV                                                                       2
  5P GAIN WILD-TYPE                                                                 6
                   vv
clus                STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE
  5P GAIN CNV                                                              0
  5P GAIN WILD-TYPE                                                        3
                   vv
clus                STOMACH ADENOCARCINOMA  SIGNET RING TYPE
  5P GAIN CNV                                              0
  5P GAIN WILD-TYPE                                        1
                   vv
clus                STOMACH ADENOCARCINOMA - DIFFUSE TYPE
  5P GAIN CNV                                           2
  5P GAIN WILD-TYPE                                    14
                   vv
clus                STOMACH ADENOCARCINOMA - NOT OTHERWISE SPECIFIED (NOS)
  5P GAIN CNV                                                            9
  5P GAIN WILD-TYPE                                                     64
                   vv
clus                STOMACH INTESTINAL ADENOCARCINOMA - MUCINOUS TYPE
  5P GAIN CNV                                                       3
  5P GAIN WILD-TYPE                                                 4
                   vv
clus                STOMACH INTESTINAL ADENOCARCINOMA - PAPILLARY TYPE
  5P GAIN CNV                                                        0
  5P GAIN WILD-TYPE                                                  3
                   vv
clus                STOMACH INTESTINAL ADENOCARCINOMA - TUBULAR TYPE
  5P GAIN CNV                                                      1
  5P GAIN WILD-TYPE                                                9
                   vv
clus                STOMACH INTESTINAL ADENOCARCINOMA - TYPE NOT OTHERWISE SPECIFIED (NOS)
  5P GAIN CNV                                                                            7
  5P GAIN WILD-TYPE                                                                     21
D8V4, multiclass
                   vv
clus                T1 T2 T3 T4
  5P GAIN CNV        0  8 10  5
  5P GAIN WILD-TYPE  6 44 46 13
D8V5, multiclass
    clus
vv   5P GAIN CNV 5P GAIN WILD-TYPE
  T1           0                 6
  T2           8                44
  T3          10                46
  T4           5                13
                   vv
clus                N0 N1 N2 N3
  5P GAIN CNV        7 10  4  3
  5P GAIN WILD-TYPE 37 39 19 12
D8V6, multiclass
    clus
vv   5P GAIN CNV 5P GAIN WILD-TYPE
  N0           7                37
  N1          10                39
  N2           4                19
  N3           3                12
                   vv
clus                M0 M1 MX
  5P GAIN CNV       21  4  0
  5P GAIN WILD-TYPE 97 12  8
D8V7, multiclass
    clus
vv   5P GAIN CNV 5P GAIN WILD-TYPE
  M0          21                97
  M1           4                12
  MX           0                 8
                   vv
clus                 I II III IV
  5P GAIN CNV        3  9   3  8
  5P GAIN WILD-TYPE 21 28  36 18
D8V8, multiclass
     clus
vv    5P GAIN CNV 5P GAIN WILD-TYPE
  I             3                21
  II            9                28
  III           3                36
  IV            8                18
D8V9, binary
[1] "tbl2"
                   cls
clus                [,1] [,2]
  5P GAIN CNV          1   27
  5P GAIN WILD-TYPE    4  148
     clus
vv    5P GAIN CNV 5P GAIN WILD-TYPE
  NO            1                 4
  YES          27               148
                   vv
clus                 R0  R1  R2  RX
  5P GAIN CNV        20   1   4   2
  5P GAIN WILD-TYPE 105   6   8  23
D8V10, multiclass
    clus
vv   5P GAIN CNV 5P GAIN WILD-TYPE
  R0          20               105
  R1           1                 6
  R2           4                 8
  RX           2                23
D8V11, continuous

Clustering(9) Variable = 5q gain
D9V1, survival
                   sevent
clus2                 0   1
  5Q GAIN CNV         6   0
  5Q GAIN WILD-TYPE 118  19
      5Q GAIN CNV 5Q GAIN WILD-TYPE 
                6               137 
      5Q GAIN CNV 5Q GAIN WILD-TYPE 
                0                19 
$`5Q GAIN CNV`
TCGA-BR-7715 TCGA-BR-8284 TCGA-CG-4436 TCGA-CG-4455 TCGA-CG-4466 TCGA-FP-7829 
        1.05         0.72        52.96        12.03        18.94         0.20 

$`5Q GAIN WILD-TYPE`
TCGA-B7-5816 TCGA-B7-5818 TCGA-BR-6452 TCGA-BR-6455 TCGA-BR-6457 TCGA-BR-6458 
        5.62         0.10         0.95         1.41         1.35         1.35 
TCGA-BR-6563 TCGA-BR-6564 TCGA-BR-6565 TCGA-BR-6566 TCGA-BR-6705 TCGA-BR-6706 
        0.85         0.82         0.62         0.62         1.71         2.17 
TCGA-BR-6707 TCGA-BR-6709 TCGA-BR-6710 TCGA-BR-6801 TCGA-BR-6802 TCGA-BR-6803 
        0.99         1.22         0.66         1.12         0.76         0.66 
TCGA-BR-6852 TCGA-BR-7196 TCGA-BR-7197 TCGA-BR-7703 TCGA-BR-7704 TCGA-BR-7707 
        0.26         1.22         1.48         0.46         1.25         0.13 
TCGA-BR-7716 TCGA-BR-7717 TCGA-BR-7722 TCGA-BR-7723 TCGA-BR-7851 TCGA-BR-7901 
        0.82         0.69         0.16         4.54         0.99         0.95 
TCGA-BR-7957 TCGA-BR-7958 TCGA-BR-7959 TCGA-BR-8059 TCGA-BR-8060 TCGA-BR-8077 
        0.69         0.16         1.08         0.82         1.32         0.69 
TCGA-BR-8078 TCGA-BR-8080 TCGA-BR-8081 TCGA-BR-8285 TCGA-BR-8286 TCGA-BR-8289 
        0.95         0.49         0.46         0.26         0.43         0.26 
TCGA-BR-8291 TCGA-BR-8295 TCGA-BR-8296 TCGA-BR-8297 TCGA-BR-8592 TCGA-BR-A4IU 
        1.18         1.55         1.48         0.76         0.20         0.59 
TCGA-BR-A4IV TCGA-BR-A4IY TCGA-BR-A4IZ TCGA-BR-A4J1 TCGA-BR-A4J2 TCGA-BR-A4J4 
        0.92         0.39         0.79         0.72         0.79         0.53 
TCGA-BR-A4J5 TCGA-BR-A4J6 TCGA-BR-A4J8 TCGA-BR-A4J9 TCGA-BR-A4PF TCGA-BR-A4QI 
        0.43         0.13         0.23         0.10         0.72         0.49 
TCGA-BR-A4QL TCGA-CD-5798 TCGA-CD-5799 TCGA-CD-5800 TCGA-CD-5801 TCGA-CD-5802 
        2.24         0.82         0.69         0.36         0.49         0.30 
TCGA-CD-5803 TCGA-CG-4300 TCGA-CG-4301 TCGA-CG-4304 TCGA-CG-4305 TCGA-CG-4306 
        0.07        20.02         3.02        27.02        15.95         1.02 
TCGA-CG-4437 TCGA-CG-4438 TCGA-CG-4440 TCGA-CG-4441 TCGA-CG-4443 TCGA-CG-4444 
        8.05        54.05         4.01        14.01        29.98        47.05 
TCGA-CG-4449 TCGA-CG-4460 TCGA-CG-4462 TCGA-CG-4465 TCGA-CG-4469 TCGA-CG-4472 
       19.07        21.99         1.02         8.98         7.07        12.00 
TCGA-CG-4474 TCGA-CG-4477 TCGA-CG-5716 TCGA-CG-5717 TCGA-CG-5718 TCGA-CG-5719 
        1.02         1.02         1.02         6.94         1.02         1.02 
TCGA-CG-5720 TCGA-CG-5721 TCGA-CG-5722 TCGA-CG-5723 TCGA-CG-5724 TCGA-CG-5725 
        0.99         5.98         0.95        70.06        12.03        15.02 
TCGA-CG-5726 TCGA-CG-5727 TCGA-CG-5728 TCGA-CG-5730 TCGA-CG-5732 TCGA-CG-5733 
       28.96        31.04        65.10         4.01        55.04        21.07 
TCGA-CG-5734 TCGA-D7-5577 TCGA-D7-5578 TCGA-D7-5579 TCGA-D7-6518 TCGA-D7-6519 
        7.99         8.65         3.58         4.54         9.80        15.65 
TCGA-D7-6520 TCGA-D7-6521 TCGA-D7-6522 TCGA-D7-6524 TCGA-D7-6525 TCGA-D7-6526 
        9.63         8.19         6.90         0.69         5.95         6.61 
TCGA-D7-6527 TCGA-D7-6528 TCGA-D7-6815 TCGA-D7-6817 TCGA-D7-6818 TCGA-D7-6820 
        4.14         1.68         3.65         4.70         4.04         2.93 
TCGA-D7-6822 TCGA-EQ-5647 TCGA-EQ-8122 TCGA-F1-6177 TCGA-F1-6874 TCGA-F1-6875 
        4.27         0.62         7.79         6.54         2.01        72.23 
TCGA-FP-7735 TCGA-FP-7916 TCGA-FP-7998 TCGA-FP-8099 TCGA-FP-8209 TCGA-FP-8210 
        0.39         3.02         3.58         1.02        59.05         5.03 
TCGA-FP-8631 TCGA-HJ-7597 TCGA-IN-7806 TCGA-IN-7808 TCGA-IP-7968 
        0.56        26.43         6.87         3.55         2.53 

      5Q GAIN CNV 5Q GAIN WILD-TYPE 
             0.20              0.07 
      5Q GAIN CNV 5Q GAIN WILD-TYPE 
            52.96             72.23 
      5Q GAIN CNV 5Q GAIN WILD-TYPE 
             6.54              1.25 
[1] "0.2 - 53.0 (6.5)" "0.1 - 72.2 (1.2)"
       TCGA-B7-5816        TCGA-B7-5818        TCGA-BR-6452        TCGA-BR-6455 
"5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" 
       TCGA-BR-6457        TCGA-BR-6458        TCGA-BR-6563        TCGA-BR-6564 
"5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" 
       TCGA-BR-6565        TCGA-BR-6566        TCGA-BR-6705        TCGA-BR-6706 
"5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" 
       TCGA-BR-6707        TCGA-BR-6709        TCGA-BR-6710        TCGA-BR-6801 
"5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" 
       TCGA-BR-6802        TCGA-BR-6803        TCGA-BR-6852        TCGA-BR-7196 
"5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" 
       TCGA-BR-7197        TCGA-BR-7703        TCGA-BR-7704        TCGA-BR-7707 
"5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" 
       TCGA-BR-7715        TCGA-BR-7716        TCGA-BR-7717        TCGA-BR-7722 
      "5Q GAIN CNV" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" 
       TCGA-BR-7723        TCGA-BR-7851        TCGA-BR-7901        TCGA-BR-7957 
"5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" 
       TCGA-BR-7958        TCGA-BR-7959        TCGA-BR-8059        TCGA-BR-8060 
"5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" 
       TCGA-BR-8077        TCGA-BR-8078        TCGA-BR-8080        TCGA-BR-8081 
"5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" 
       TCGA-BR-8284        TCGA-BR-8285        TCGA-BR-8286        TCGA-BR-8289 
      "5Q GAIN CNV" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" 
       TCGA-BR-8291        TCGA-BR-8295        TCGA-BR-8296        TCGA-BR-8297 
"5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" 
       TCGA-BR-8592        TCGA-BR-A4IU        TCGA-BR-A4IV        TCGA-BR-A4IY 
"5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" 
       TCGA-BR-A4IZ        TCGA-BR-A4J1        TCGA-BR-A4J2        TCGA-BR-A4J4 
"5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" 
       TCGA-BR-A4J5        TCGA-BR-A4J6        TCGA-BR-A4J8        TCGA-BR-A4J9 
"5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" 
       TCGA-BR-A4PF        TCGA-BR-A4QI        TCGA-BR-A4QL        TCGA-CD-5798 
"5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" 
       TCGA-CD-5799        TCGA-CD-5800        TCGA-CD-5801        TCGA-CD-5802 
"5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" 
       TCGA-CD-5803        TCGA-CG-4300        TCGA-CG-4301        TCGA-CG-4304 
"5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" 
       TCGA-CG-4305        TCGA-CG-4306        TCGA-CG-4436        TCGA-CG-4437 
"5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE"       "5Q GAIN CNV" "5Q GAIN WILD-TYPE" 
       TCGA-CG-4438        TCGA-CG-4440        TCGA-CG-4441        TCGA-CG-4443 
"5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" 
       TCGA-CG-4444        TCGA-CG-4449        TCGA-CG-4455        TCGA-CG-4460 
"5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE"       "5Q GAIN CNV" "5Q GAIN WILD-TYPE" 
       TCGA-CG-4462        TCGA-CG-4465        TCGA-CG-4466        TCGA-CG-4469 
"5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE"       "5Q GAIN CNV" "5Q GAIN WILD-TYPE" 
       TCGA-CG-4472        TCGA-CG-4474        TCGA-CG-4477        TCGA-CG-5716 
"5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" 
       TCGA-CG-5717        TCGA-CG-5718        TCGA-CG-5719        TCGA-CG-5720 
"5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" 
       TCGA-CG-5721        TCGA-CG-5722        TCGA-CG-5723        TCGA-CG-5724 
"5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" 
       TCGA-CG-5725        TCGA-CG-5726        TCGA-CG-5727        TCGA-CG-5728 
"5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" 
       TCGA-CG-5730        TCGA-CG-5732        TCGA-CG-5733        TCGA-CG-5734 
"5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" 
       TCGA-D7-5577        TCGA-D7-5578        TCGA-D7-5579        TCGA-D7-6518 
"5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" 
       TCGA-D7-6519        TCGA-D7-6520        TCGA-D7-6521        TCGA-D7-6522 
"5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" 
       TCGA-D7-6524        TCGA-D7-6525        TCGA-D7-6526        TCGA-D7-6527 
"5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" 
       TCGA-D7-6528        TCGA-D7-6815        TCGA-D7-6817        TCGA-D7-6818 
"5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" 
       TCGA-D7-6820        TCGA-D7-6822        TCGA-EQ-5647        TCGA-EQ-8122 
"5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" 
       TCGA-F1-6177        TCGA-F1-6874        TCGA-F1-6875        TCGA-FP-7735 
"5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" 
       TCGA-FP-7829        TCGA-FP-7916        TCGA-FP-7998        TCGA-FP-8099 
      "5Q GAIN CNV" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" 
       TCGA-FP-8209        TCGA-FP-8210        TCGA-FP-8631        TCGA-HJ-7597 
"5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" 
       TCGA-IN-7806        TCGA-IN-7808        TCGA-IP-7968 
"5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" 
       TCGA-B7-5816        TCGA-B7-5818        TCGA-BR-6452        TCGA-BR-6455 
"5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" 
       TCGA-BR-6457        TCGA-BR-6458        TCGA-BR-6563        TCGA-BR-6564 
"5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" 
       TCGA-BR-6565        TCGA-BR-6566        TCGA-BR-6705        TCGA-BR-6706 
"5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" 
       TCGA-BR-6707        TCGA-BR-6709        TCGA-BR-6710        TCGA-BR-6801 
"5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" 
       TCGA-BR-6802        TCGA-BR-6803        TCGA-BR-6852        TCGA-BR-7196 
"5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" 
       TCGA-BR-7197        TCGA-BR-7703        TCGA-BR-7704        TCGA-BR-7707 
"5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" 
       TCGA-BR-7715        TCGA-BR-7716        TCGA-BR-7717        TCGA-BR-7722 
      "5Q GAIN CNV" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" 
       TCGA-BR-7723        TCGA-BR-7851        TCGA-BR-7901        TCGA-BR-7957 
"5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" 
       TCGA-BR-7958        TCGA-BR-7959        TCGA-BR-8059        TCGA-BR-8060 
"5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" 
       TCGA-BR-8077        TCGA-BR-8078        TCGA-BR-8080        TCGA-BR-8081 
"5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" 
       TCGA-BR-8284        TCGA-BR-8285        TCGA-BR-8286        TCGA-BR-8289 
      "5Q GAIN CNV" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" 
       TCGA-BR-8291        TCGA-BR-8295        TCGA-BR-8296        TCGA-BR-8297 
"5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" 
       TCGA-BR-8592        TCGA-BR-A4IU        TCGA-BR-A4IV        TCGA-BR-A4IY 
"5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" 
       TCGA-BR-A4IZ        TCGA-BR-A4J1        TCGA-BR-A4J2        TCGA-BR-A4J4 
"5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" 
       TCGA-BR-A4J5        TCGA-BR-A4J6        TCGA-BR-A4J8        TCGA-BR-A4J9 
"5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" 
       TCGA-BR-A4PF        TCGA-BR-A4QI        TCGA-BR-A4QL        TCGA-CD-5798 
"5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" 
       TCGA-CD-5799        TCGA-CD-5800        TCGA-CD-5801        TCGA-CD-5802 
"5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" 
       TCGA-CD-5803        TCGA-CG-4300        TCGA-CG-4301        TCGA-CG-4304 
"5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" 
       TCGA-CG-4305        TCGA-CG-4306        TCGA-CG-4436        TCGA-CG-4437 
"5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE"       "5Q GAIN CNV" "5Q GAIN WILD-TYPE" 
       TCGA-CG-4438        TCGA-CG-4440        TCGA-CG-4441        TCGA-CG-4443 
"5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" 
       TCGA-CG-4444        TCGA-CG-4449        TCGA-CG-4455        TCGA-CG-4460 
"5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE"       "5Q GAIN CNV" "5Q GAIN WILD-TYPE" 
       TCGA-CG-4462        TCGA-CG-4465        TCGA-CG-4466        TCGA-CG-4469 
"5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE"       "5Q GAIN CNV" "5Q GAIN WILD-TYPE" 
       TCGA-CG-4472        TCGA-CG-4474        TCGA-CG-4477        TCGA-CG-5716 
"5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" 
       TCGA-CG-5717        TCGA-CG-5718        TCGA-CG-5719        TCGA-CG-5720 
"5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" 
       TCGA-CG-5721        TCGA-CG-5722        TCGA-CG-5723        TCGA-CG-5724 
"5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" 
       TCGA-CG-5725        TCGA-CG-5726        TCGA-CG-5727        TCGA-CG-5728 
"5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" 
       TCGA-CG-5730        TCGA-CG-5732        TCGA-CG-5733        TCGA-CG-5734 
"5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" 
       TCGA-D7-5577        TCGA-D7-5578        TCGA-D7-5579        TCGA-D7-6518 
"5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" 
       TCGA-D7-6519        TCGA-D7-6520        TCGA-D7-6521        TCGA-D7-6522 
"5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" 
       TCGA-D7-6524        TCGA-D7-6525        TCGA-D7-6526        TCGA-D7-6527 
"5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" 
       TCGA-D7-6528        TCGA-D7-6815        TCGA-D7-6817        TCGA-D7-6818 
"5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" 
       TCGA-D7-6820        TCGA-D7-6822        TCGA-EQ-5647        TCGA-EQ-8122 
"5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" 
       TCGA-F1-6177        TCGA-F1-6874        TCGA-F1-6875        TCGA-FP-7735 
"5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" 
       TCGA-FP-7829        TCGA-FP-7916        TCGA-FP-7998        TCGA-FP-8099 
      "5Q GAIN CNV" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" 
       TCGA-FP-8209        TCGA-FP-8210        TCGA-FP-8631        TCGA-HJ-7597 
"5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" 
       TCGA-IN-7806        TCGA-IN-7808        TCGA-IP-7968 
"5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" 
       TCGA-B7-5816        TCGA-B7-5818        TCGA-BR-6452        TCGA-BR-6455 
"5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" 
       TCGA-BR-6457        TCGA-BR-6458        TCGA-BR-6563        TCGA-BR-6564 
"5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" 
       TCGA-BR-6565        TCGA-BR-6566        TCGA-BR-6705        TCGA-BR-6706 
"5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" 
       TCGA-BR-6707        TCGA-BR-6709        TCGA-BR-6710        TCGA-BR-6801 
"5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" 
       TCGA-BR-6802        TCGA-BR-6803        TCGA-BR-6852        TCGA-BR-7196 
"5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" 
       TCGA-BR-7197        TCGA-BR-7703        TCGA-BR-7704        TCGA-BR-7707 
"5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" 
       TCGA-BR-7715        TCGA-BR-7716        TCGA-BR-7717        TCGA-BR-7722 
      "5Q GAIN CNV" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" 
       TCGA-BR-7723        TCGA-BR-7851        TCGA-BR-7901        TCGA-BR-7957 
"5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" 
       TCGA-BR-7958        TCGA-BR-7959        TCGA-BR-8059        TCGA-BR-8060 
"5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" 
       TCGA-BR-8077        TCGA-BR-8078        TCGA-BR-8080        TCGA-BR-8081 
"5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" 
       TCGA-BR-8284        TCGA-BR-8285        TCGA-BR-8286        TCGA-BR-8289 
      "5Q GAIN CNV" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" 
       TCGA-BR-8291        TCGA-BR-8295        TCGA-BR-8296        TCGA-BR-8297 
"5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" 
       TCGA-BR-8592        TCGA-BR-A4IU        TCGA-BR-A4IV        TCGA-BR-A4IY 
"5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" 
       TCGA-BR-A4IZ        TCGA-BR-A4J1        TCGA-BR-A4J2        TCGA-BR-A4J4 
"5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" 
       TCGA-BR-A4J5        TCGA-BR-A4J6        TCGA-BR-A4J8        TCGA-BR-A4J9 
"5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" 
       TCGA-BR-A4PF        TCGA-BR-A4QI        TCGA-BR-A4QL        TCGA-CD-5798 
"5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" 
       TCGA-CD-5799        TCGA-CD-5800        TCGA-CD-5801        TCGA-CD-5802 
"5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" 
       TCGA-CD-5803        TCGA-CG-4300        TCGA-CG-4301        TCGA-CG-4304 
"5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" 
       TCGA-CG-4305        TCGA-CG-4306        TCGA-CG-4436        TCGA-CG-4437 
"5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE"       "5Q GAIN CNV" "5Q GAIN WILD-TYPE" 
       TCGA-CG-4438        TCGA-CG-4440        TCGA-CG-4441        TCGA-CG-4443 
"5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" 
       TCGA-CG-4444        TCGA-CG-4449        TCGA-CG-4455        TCGA-CG-4460 
"5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE"       "5Q GAIN CNV" "5Q GAIN WILD-TYPE" 
       TCGA-CG-4462        TCGA-CG-4465        TCGA-CG-4466        TCGA-CG-4469 
"5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE"       "5Q GAIN CNV" "5Q GAIN WILD-TYPE" 
       TCGA-CG-4472        TCGA-CG-4474        TCGA-CG-4477        TCGA-CG-5716 
"5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" 
       TCGA-CG-5717        TCGA-CG-5718        TCGA-CG-5719        TCGA-CG-5720 
"5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" 
       TCGA-CG-5721        TCGA-CG-5722        TCGA-CG-5723        TCGA-CG-5724 
"5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" 
       TCGA-CG-5725        TCGA-CG-5726        TCGA-CG-5727        TCGA-CG-5728 
"5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" 
       TCGA-CG-5730        TCGA-CG-5732        TCGA-CG-5733        TCGA-CG-5734 
"5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" 
       TCGA-D7-5577        TCGA-D7-5578        TCGA-D7-5579        TCGA-D7-6518 
"5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" 
       TCGA-D7-6519        TCGA-D7-6520        TCGA-D7-6521        TCGA-D7-6522 
"5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" 
       TCGA-D7-6524        TCGA-D7-6525        TCGA-D7-6526        TCGA-D7-6527 
"5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" 
       TCGA-D7-6528        TCGA-D7-6815        TCGA-D7-6817        TCGA-D7-6818 
"5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" 
       TCGA-D7-6820        TCGA-D7-6822        TCGA-EQ-5647        TCGA-EQ-8122 
"5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" 
       TCGA-F1-6177        TCGA-F1-6874        TCGA-F1-6875        TCGA-FP-7735 
"5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" 
       TCGA-FP-7829        TCGA-FP-7916        TCGA-FP-7998        TCGA-FP-8099 
      "5Q GAIN CNV" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" 
       TCGA-FP-8209        TCGA-FP-8210        TCGA-FP-8631        TCGA-HJ-7597 
"5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" 
       TCGA-IN-7806        TCGA-IN-7808        TCGA-IP-7968 
"5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" 
[1] "hr="     "7.5e+07"
D9V2, continuous
D9V3, binary
[1] "tbl2"
                   cls
clus                [,1] [,2]
  5Q GAIN CNV          2    5
  5Q GAIN WILD-TYPE   70  103
        clus
vv       5Q GAIN CNV 5Q GAIN WILD-TYPE
  FEMALE           2                70
  MALE             5               103
                   vv
clus                STOMACH  ADENOCARCINOMA  DIFFUSE TYPE
  5Q GAIN CNV                                           0
  5Q GAIN WILD-TYPE                                    10
                   vv
clus                STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  5Q GAIN CNV                                                            0
  5Q GAIN WILD-TYPE                                                     16
                   vv
clus                STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  5Q GAIN CNV                                                                       1
  5Q GAIN WILD-TYPE                                                                 7
                   vv
clus                STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE
  5Q GAIN CNV                                                              0
  5Q GAIN WILD-TYPE                                                        3
                   vv
clus                STOMACH ADENOCARCINOMA  SIGNET RING TYPE
  5Q GAIN CNV                                              0
  5Q GAIN WILD-TYPE                                        1
                   vv
clus                STOMACH ADENOCARCINOMA - DIFFUSE TYPE
  5Q GAIN CNV                                           0
  5Q GAIN WILD-TYPE                                    16
                   vv
clus                STOMACH ADENOCARCINOMA - NOT OTHERWISE SPECIFIED (NOS)
  5Q GAIN CNV                                                            2
  5Q GAIN WILD-TYPE                                                     71
                   vv
clus                STOMACH INTESTINAL ADENOCARCINOMA - MUCINOUS TYPE
  5Q GAIN CNV                                                       2
  5Q GAIN WILD-TYPE                                                 5
                   vv
clus                STOMACH INTESTINAL ADENOCARCINOMA - PAPILLARY TYPE
  5Q GAIN CNV                                                        0
  5Q GAIN WILD-TYPE                                                  3
                   vv
clus                STOMACH INTESTINAL ADENOCARCINOMA - TUBULAR TYPE
  5Q GAIN CNV                                                      0
  5Q GAIN WILD-TYPE                                               10
                   vv
clus                STOMACH INTESTINAL ADENOCARCINOMA - TYPE NOT OTHERWISE SPECIFIED (NOS)
  5Q GAIN CNV                                                                            2
  5Q GAIN WILD-TYPE                                                                     26
D9V4, multiclass
                   vv
clus                T1 T2 T3 T4
  5Q GAIN CNV        0  3  3  0
  5Q GAIN WILD-TYPE  6 49 53 18
D9V5, multiclass
    clus
vv   5Q GAIN CNV 5Q GAIN WILD-TYPE
  T1           0                 6
  T2           3                49
  T3           3                53
  T4           0                18
                   vv
clus                N0 N1 N2 N3
  5Q GAIN CNV        4  2  0  0
  5Q GAIN WILD-TYPE 40 47 23 15
D9V6, multiclass
    clus
vv   5Q GAIN CNV 5Q GAIN WILD-TYPE
  N0           4                40
  N1           2                47
  N2           0                23
  N3           0                15
                   vv
clus                 M0  M1  MX
  5Q GAIN CNV         6   0   0
  5Q GAIN WILD-TYPE 112  16   8
D9V7, multiclass
    clus
vv   5Q GAIN CNV 5Q GAIN WILD-TYPE
  M0           6               112
  M1           0                16
  MX           0                 8
                   vv
clus                 I II III IV
  5Q GAIN CNV        2  3   1  0
  5Q GAIN WILD-TYPE 22 34  38 26
D9V8, multiclass
     clus
vv    5Q GAIN CNV 5Q GAIN WILD-TYPE
  I             2                22
  II            3                34
  III           1                38
  IV            0                26
D9V9, binary
[1] "tbl2"
                   cls
clus                [,1] [,2]
  5Q GAIN CNV          0    7
  5Q GAIN WILD-TYPE    5  168
     clus
vv    5Q GAIN CNV 5Q GAIN WILD-TYPE
  NO            0                 5
  YES           7               168
                   vv
clus                 R0  R1  R2  RX
  5Q GAIN CNV         7   0   0   0
  5Q GAIN WILD-TYPE 118   7  12  25
D9V10, multiclass
    clus
vv   5Q GAIN CNV 5Q GAIN WILD-TYPE
  R0           7               118
  R1           0                 7
  R2           0                12
  RX           0                25
D9V11, continuous

Clustering(10) Variable = 6p gain
D10V1, survival
                   sevent
clus2                 0   1
  6P GAIN CNV        10   1
  6P GAIN WILD-TYPE 114  18
      6P GAIN CNV 6P GAIN WILD-TYPE 
               11               132 
      6P GAIN CNV 6P GAIN WILD-TYPE 
                1                18 
$`6P GAIN CNV`
TCGA-BR-7197 TCGA-BR-7704 TCGA-BR-7715 TCGA-BR-7717 TCGA-BR-7723 TCGA-BR-8286 
        1.48         1.25         1.05         0.69         4.54         0.43 
TCGA-CG-4438 TCGA-CG-4460 TCGA-D7-6822 TCGA-EQ-8122 TCGA-FP-8631 
       54.05        21.99         4.27         7.79         0.56 

$`6P GAIN WILD-TYPE`
TCGA-B7-5816 TCGA-B7-5818 TCGA-BR-6452 TCGA-BR-6455 TCGA-BR-6457 TCGA-BR-6458 
        5.62         0.10         0.95         1.41         1.35         1.35 
TCGA-BR-6563 TCGA-BR-6564 TCGA-BR-6565 TCGA-BR-6566 TCGA-BR-6705 TCGA-BR-6706 
        0.85         0.82         0.62         0.62         1.71         2.17 
TCGA-BR-6707 TCGA-BR-6709 TCGA-BR-6710 TCGA-BR-6801 TCGA-BR-6802 TCGA-BR-6803 
        0.99         1.22         0.66         1.12         0.76         0.66 
TCGA-BR-6852 TCGA-BR-7196 TCGA-BR-7703 TCGA-BR-7707 TCGA-BR-7716 TCGA-BR-7722 
        0.26         1.22         0.46         0.13         0.82         0.16 
TCGA-BR-7851 TCGA-BR-7901 TCGA-BR-7957 TCGA-BR-7958 TCGA-BR-7959 TCGA-BR-8059 
        0.99         0.95         0.69         0.16         1.08         0.82 
TCGA-BR-8060 TCGA-BR-8077 TCGA-BR-8078 TCGA-BR-8080 TCGA-BR-8081 TCGA-BR-8284 
        1.32         0.69         0.95         0.49         0.46         0.72 
TCGA-BR-8285 TCGA-BR-8289 TCGA-BR-8291 TCGA-BR-8295 TCGA-BR-8296 TCGA-BR-8297 
        0.26         0.26         1.18         1.55         1.48         0.76 
TCGA-BR-8592 TCGA-BR-A4IU TCGA-BR-A4IV TCGA-BR-A4IY TCGA-BR-A4IZ TCGA-BR-A4J1 
        0.20         0.59         0.92         0.39         0.79         0.72 
TCGA-BR-A4J2 TCGA-BR-A4J4 TCGA-BR-A4J5 TCGA-BR-A4J6 TCGA-BR-A4J8 TCGA-BR-A4J9 
        0.79         0.53         0.43         0.13         0.23         0.10 
TCGA-BR-A4PF TCGA-BR-A4QI TCGA-BR-A4QL TCGA-CD-5798 TCGA-CD-5799 TCGA-CD-5800 
        0.72         0.49         2.24         0.82         0.69         0.36 
TCGA-CD-5801 TCGA-CD-5802 TCGA-CD-5803 TCGA-CG-4300 TCGA-CG-4301 TCGA-CG-4304 
        0.49         0.30         0.07        20.02         3.02        27.02 
TCGA-CG-4305 TCGA-CG-4306 TCGA-CG-4436 TCGA-CG-4437 TCGA-CG-4440 TCGA-CG-4441 
       15.95         1.02        52.96         8.05         4.01        14.01 
TCGA-CG-4443 TCGA-CG-4444 TCGA-CG-4449 TCGA-CG-4455 TCGA-CG-4462 TCGA-CG-4465 
       29.98        47.05        19.07        12.03         1.02         8.98 
TCGA-CG-4466 TCGA-CG-4469 TCGA-CG-4472 TCGA-CG-4474 TCGA-CG-4477 TCGA-CG-5716 
       18.94         7.07        12.00         1.02         1.02         1.02 
TCGA-CG-5717 TCGA-CG-5718 TCGA-CG-5719 TCGA-CG-5720 TCGA-CG-5721 TCGA-CG-5722 
        6.94         1.02         1.02         0.99         5.98         0.95 
TCGA-CG-5723 TCGA-CG-5724 TCGA-CG-5725 TCGA-CG-5726 TCGA-CG-5727 TCGA-CG-5728 
       70.06        12.03        15.02        28.96        31.04        65.10 
TCGA-CG-5730 TCGA-CG-5732 TCGA-CG-5733 TCGA-CG-5734 TCGA-D7-5577 TCGA-D7-5578 
        4.01        55.04        21.07         7.99         8.65         3.58 
TCGA-D7-5579 TCGA-D7-6518 TCGA-D7-6519 TCGA-D7-6520 TCGA-D7-6521 TCGA-D7-6522 
        4.54         9.80        15.65         9.63         8.19         6.90 
TCGA-D7-6524 TCGA-D7-6525 TCGA-D7-6526 TCGA-D7-6527 TCGA-D7-6528 TCGA-D7-6815 
        0.69         5.95         6.61         4.14         1.68         3.65 
TCGA-D7-6817 TCGA-D7-6818 TCGA-D7-6820 TCGA-EQ-5647 TCGA-F1-6177 TCGA-F1-6874 
        4.70         4.04         2.93         0.62         6.54         2.01 
TCGA-F1-6875 TCGA-FP-7735 TCGA-FP-7829 TCGA-FP-7916 TCGA-FP-7998 TCGA-FP-8099 
       72.23         0.39         0.20         3.02         3.58         1.02 
TCGA-FP-8209 TCGA-FP-8210 TCGA-HJ-7597 TCGA-IN-7806 TCGA-IN-7808 TCGA-IP-7968 
       59.05         5.03        26.43         6.87         3.55         2.53 

      6P GAIN CNV 6P GAIN WILD-TYPE 
             0.43              0.07 
      6P GAIN CNV 6P GAIN WILD-TYPE 
            54.05             72.23 
      6P GAIN CNV 6P GAIN WILD-TYPE 
             1.48              1.22 
[1] "0.4 - 54.0 (1.5)" "0.1 - 72.2 (1.2)"
       TCGA-B7-5816        TCGA-B7-5818        TCGA-BR-6452        TCGA-BR-6455 
"6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" 
       TCGA-BR-6457        TCGA-BR-6458        TCGA-BR-6563        TCGA-BR-6564 
"6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" 
       TCGA-BR-6565        TCGA-BR-6566        TCGA-BR-6705        TCGA-BR-6706 
"6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" 
       TCGA-BR-6707        TCGA-BR-6709        TCGA-BR-6710        TCGA-BR-6801 
"6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" 
       TCGA-BR-6802        TCGA-BR-6803        TCGA-BR-6852        TCGA-BR-7196 
"6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" 
       TCGA-BR-7197        TCGA-BR-7703        TCGA-BR-7704        TCGA-BR-7707 
      "6P GAIN CNV" "6P GAIN WILD-TYPE"       "6P GAIN CNV" "6P GAIN WILD-TYPE" 
       TCGA-BR-7715        TCGA-BR-7716        TCGA-BR-7717        TCGA-BR-7722 
      "6P GAIN CNV" "6P GAIN WILD-TYPE"       "6P GAIN CNV" "6P GAIN WILD-TYPE" 
       TCGA-BR-7723        TCGA-BR-7851        TCGA-BR-7901        TCGA-BR-7957 
      "6P GAIN CNV" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" 
       TCGA-BR-7958        TCGA-BR-7959        TCGA-BR-8059        TCGA-BR-8060 
"6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" 
       TCGA-BR-8077        TCGA-BR-8078        TCGA-BR-8080        TCGA-BR-8081 
"6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" 
       TCGA-BR-8284        TCGA-BR-8285        TCGA-BR-8286        TCGA-BR-8289 
"6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE"       "6P GAIN CNV" "6P GAIN WILD-TYPE" 
       TCGA-BR-8291        TCGA-BR-8295        TCGA-BR-8296        TCGA-BR-8297 
"6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" 
       TCGA-BR-8592        TCGA-BR-A4IU        TCGA-BR-A4IV        TCGA-BR-A4IY 
"6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" 
       TCGA-BR-A4IZ        TCGA-BR-A4J1        TCGA-BR-A4J2        TCGA-BR-A4J4 
"6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" 
       TCGA-BR-A4J5        TCGA-BR-A4J6        TCGA-BR-A4J8        TCGA-BR-A4J9 
"6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" 
       TCGA-BR-A4PF        TCGA-BR-A4QI        TCGA-BR-A4QL        TCGA-CD-5798 
"6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" 
       TCGA-CD-5799        TCGA-CD-5800        TCGA-CD-5801        TCGA-CD-5802 
"6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" 
       TCGA-CD-5803        TCGA-CG-4300        TCGA-CG-4301        TCGA-CG-4304 
"6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" 
       TCGA-CG-4305        TCGA-CG-4306        TCGA-CG-4436        TCGA-CG-4437 
"6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" 
       TCGA-CG-4438        TCGA-CG-4440        TCGA-CG-4441        TCGA-CG-4443 
      "6P GAIN CNV" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" 
       TCGA-CG-4444        TCGA-CG-4449        TCGA-CG-4455        TCGA-CG-4460 
"6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE"       "6P GAIN CNV" 
       TCGA-CG-4462        TCGA-CG-4465        TCGA-CG-4466        TCGA-CG-4469 
"6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" 
       TCGA-CG-4472        TCGA-CG-4474        TCGA-CG-4477        TCGA-CG-5716 
"6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" 
       TCGA-CG-5717        TCGA-CG-5718        TCGA-CG-5719        TCGA-CG-5720 
"6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" 
       TCGA-CG-5721        TCGA-CG-5722        TCGA-CG-5723        TCGA-CG-5724 
"6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" 
       TCGA-CG-5725        TCGA-CG-5726        TCGA-CG-5727        TCGA-CG-5728 
"6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" 
       TCGA-CG-5730        TCGA-CG-5732        TCGA-CG-5733        TCGA-CG-5734 
"6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" 
       TCGA-D7-5577        TCGA-D7-5578        TCGA-D7-5579        TCGA-D7-6518 
"6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" 
       TCGA-D7-6519        TCGA-D7-6520        TCGA-D7-6521        TCGA-D7-6522 
"6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" 
       TCGA-D7-6524        TCGA-D7-6525        TCGA-D7-6526        TCGA-D7-6527 
"6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" 
       TCGA-D7-6528        TCGA-D7-6815        TCGA-D7-6817        TCGA-D7-6818 
"6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" 
       TCGA-D7-6820        TCGA-D7-6822        TCGA-EQ-5647        TCGA-EQ-8122 
"6P GAIN WILD-TYPE"       "6P GAIN CNV" "6P GAIN WILD-TYPE"       "6P GAIN CNV" 
       TCGA-F1-6177        TCGA-F1-6874        TCGA-F1-6875        TCGA-FP-7735 
"6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" 
       TCGA-FP-7829        TCGA-FP-7916        TCGA-FP-7998        TCGA-FP-8099 
"6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" 
       TCGA-FP-8209        TCGA-FP-8210        TCGA-FP-8631        TCGA-HJ-7597 
"6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE"       "6P GAIN CNV" "6P GAIN WILD-TYPE" 
       TCGA-IN-7806        TCGA-IN-7808        TCGA-IP-7968 
"6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" 
       TCGA-B7-5816        TCGA-B7-5818        TCGA-BR-6452        TCGA-BR-6455 
"6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" 
       TCGA-BR-6457        TCGA-BR-6458        TCGA-BR-6563        TCGA-BR-6564 
"6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" 
       TCGA-BR-6565        TCGA-BR-6566        TCGA-BR-6705        TCGA-BR-6706 
"6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" 
       TCGA-BR-6707        TCGA-BR-6709        TCGA-BR-6710        TCGA-BR-6801 
"6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" 
       TCGA-BR-6802        TCGA-BR-6803        TCGA-BR-6852        TCGA-BR-7196 
"6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" 
       TCGA-BR-7197        TCGA-BR-7703        TCGA-BR-7704        TCGA-BR-7707 
      "6P GAIN CNV" "6P GAIN WILD-TYPE"       "6P GAIN CNV" "6P GAIN WILD-TYPE" 
       TCGA-BR-7715        TCGA-BR-7716        TCGA-BR-7717        TCGA-BR-7722 
      "6P GAIN CNV" "6P GAIN WILD-TYPE"       "6P GAIN CNV" "6P GAIN WILD-TYPE" 
       TCGA-BR-7723        TCGA-BR-7851        TCGA-BR-7901        TCGA-BR-7957 
      "6P GAIN CNV" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" 
       TCGA-BR-7958        TCGA-BR-7959        TCGA-BR-8059        TCGA-BR-8060 
"6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" 
       TCGA-BR-8077        TCGA-BR-8078        TCGA-BR-8080        TCGA-BR-8081 
"6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" 
       TCGA-BR-8284        TCGA-BR-8285        TCGA-BR-8286        TCGA-BR-8289 
"6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE"       "6P GAIN CNV" "6P GAIN WILD-TYPE" 
       TCGA-BR-8291        TCGA-BR-8295        TCGA-BR-8296        TCGA-BR-8297 
"6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" 
       TCGA-BR-8592        TCGA-BR-A4IU        TCGA-BR-A4IV        TCGA-BR-A4IY 
"6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" 
       TCGA-BR-A4IZ        TCGA-BR-A4J1        TCGA-BR-A4J2        TCGA-BR-A4J4 
"6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" 
       TCGA-BR-A4J5        TCGA-BR-A4J6        TCGA-BR-A4J8        TCGA-BR-A4J9 
"6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" 
       TCGA-BR-A4PF        TCGA-BR-A4QI        TCGA-BR-A4QL        TCGA-CD-5798 
"6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" 
       TCGA-CD-5799        TCGA-CD-5800        TCGA-CD-5801        TCGA-CD-5802 
"6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" 
       TCGA-CD-5803        TCGA-CG-4300        TCGA-CG-4301        TCGA-CG-4304 
"6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" 
       TCGA-CG-4305        TCGA-CG-4306        TCGA-CG-4436        TCGA-CG-4437 
"6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" 
       TCGA-CG-4438        TCGA-CG-4440        TCGA-CG-4441        TCGA-CG-4443 
      "6P GAIN CNV" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" 
       TCGA-CG-4444        TCGA-CG-4449        TCGA-CG-4455        TCGA-CG-4460 
"6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE"       "6P GAIN CNV" 
       TCGA-CG-4462        TCGA-CG-4465        TCGA-CG-4466        TCGA-CG-4469 
"6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" 
       TCGA-CG-4472        TCGA-CG-4474        TCGA-CG-4477        TCGA-CG-5716 
"6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" 
       TCGA-CG-5717        TCGA-CG-5718        TCGA-CG-5719        TCGA-CG-5720 
"6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" 
       TCGA-CG-5721        TCGA-CG-5722        TCGA-CG-5723        TCGA-CG-5724 
"6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" 
       TCGA-CG-5725        TCGA-CG-5726        TCGA-CG-5727        TCGA-CG-5728 
"6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" 
       TCGA-CG-5730        TCGA-CG-5732        TCGA-CG-5733        TCGA-CG-5734 
"6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" 
       TCGA-D7-5577        TCGA-D7-5578        TCGA-D7-5579        TCGA-D7-6518 
"6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" 
       TCGA-D7-6519        TCGA-D7-6520        TCGA-D7-6521        TCGA-D7-6522 
"6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" 
       TCGA-D7-6524        TCGA-D7-6525        TCGA-D7-6526        TCGA-D7-6527 
"6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" 
       TCGA-D7-6528        TCGA-D7-6815        TCGA-D7-6817        TCGA-D7-6818 
"6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" 
       TCGA-D7-6820        TCGA-D7-6822        TCGA-EQ-5647        TCGA-EQ-8122 
"6P GAIN WILD-TYPE"       "6P GAIN CNV" "6P GAIN WILD-TYPE"       "6P GAIN CNV" 
       TCGA-F1-6177        TCGA-F1-6874        TCGA-F1-6875        TCGA-FP-7735 
"6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" 
       TCGA-FP-7829        TCGA-FP-7916        TCGA-FP-7998        TCGA-FP-8099 
"6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" 
       TCGA-FP-8209        TCGA-FP-8210        TCGA-FP-8631        TCGA-HJ-7597 
"6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE"       "6P GAIN CNV" "6P GAIN WILD-TYPE" 
       TCGA-IN-7806        TCGA-IN-7808        TCGA-IP-7968 
"6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" 
       TCGA-B7-5816        TCGA-B7-5818        TCGA-BR-6452        TCGA-BR-6455 
"6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" 
       TCGA-BR-6457        TCGA-BR-6458        TCGA-BR-6563        TCGA-BR-6564 
"6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" 
       TCGA-BR-6565        TCGA-BR-6566        TCGA-BR-6705        TCGA-BR-6706 
"6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" 
       TCGA-BR-6707        TCGA-BR-6709        TCGA-BR-6710        TCGA-BR-6801 
"6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" 
       TCGA-BR-6802        TCGA-BR-6803        TCGA-BR-6852        TCGA-BR-7196 
"6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" 
       TCGA-BR-7197        TCGA-BR-7703        TCGA-BR-7704        TCGA-BR-7707 
      "6P GAIN CNV" "6P GAIN WILD-TYPE"       "6P GAIN CNV" "6P GAIN WILD-TYPE" 
       TCGA-BR-7715        TCGA-BR-7716        TCGA-BR-7717        TCGA-BR-7722 
      "6P GAIN CNV" "6P GAIN WILD-TYPE"       "6P GAIN CNV" "6P GAIN WILD-TYPE" 
       TCGA-BR-7723        TCGA-BR-7851        TCGA-BR-7901        TCGA-BR-7957 
      "6P GAIN CNV" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" 
       TCGA-BR-7958        TCGA-BR-7959        TCGA-BR-8059        TCGA-BR-8060 
"6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" 
       TCGA-BR-8077        TCGA-BR-8078        TCGA-BR-8080        TCGA-BR-8081 
"6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" 
       TCGA-BR-8284        TCGA-BR-8285        TCGA-BR-8286        TCGA-BR-8289 
"6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE"       "6P GAIN CNV" "6P GAIN WILD-TYPE" 
       TCGA-BR-8291        TCGA-BR-8295        TCGA-BR-8296        TCGA-BR-8297 
"6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" 
       TCGA-BR-8592        TCGA-BR-A4IU        TCGA-BR-A4IV        TCGA-BR-A4IY 
"6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" 
       TCGA-BR-A4IZ        TCGA-BR-A4J1        TCGA-BR-A4J2        TCGA-BR-A4J4 
"6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" 
       TCGA-BR-A4J5        TCGA-BR-A4J6        TCGA-BR-A4J8        TCGA-BR-A4J9 
"6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" 
       TCGA-BR-A4PF        TCGA-BR-A4QI        TCGA-BR-A4QL        TCGA-CD-5798 
"6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" 
       TCGA-CD-5799        TCGA-CD-5800        TCGA-CD-5801        TCGA-CD-5802 
"6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" 
       TCGA-CD-5803        TCGA-CG-4300        TCGA-CG-4301        TCGA-CG-4304 
"6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" 
       TCGA-CG-4305        TCGA-CG-4306        TCGA-CG-4436        TCGA-CG-4437 
"6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" 
       TCGA-CG-4438        TCGA-CG-4440        TCGA-CG-4441        TCGA-CG-4443 
      "6P GAIN CNV" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" 
       TCGA-CG-4444        TCGA-CG-4449        TCGA-CG-4455        TCGA-CG-4460 
"6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE"       "6P GAIN CNV" 
       TCGA-CG-4462        TCGA-CG-4465        TCGA-CG-4466        TCGA-CG-4469 
"6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" 
       TCGA-CG-4472        TCGA-CG-4474        TCGA-CG-4477        TCGA-CG-5716 
"6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" 
       TCGA-CG-5717        TCGA-CG-5718        TCGA-CG-5719        TCGA-CG-5720 
"6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" 
       TCGA-CG-5721        TCGA-CG-5722        TCGA-CG-5723        TCGA-CG-5724 
"6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" 
       TCGA-CG-5725        TCGA-CG-5726        TCGA-CG-5727        TCGA-CG-5728 
"6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" 
       TCGA-CG-5730        TCGA-CG-5732        TCGA-CG-5733        TCGA-CG-5734 
"6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" 
       TCGA-D7-5577        TCGA-D7-5578        TCGA-D7-5579        TCGA-D7-6518 
"6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" 
       TCGA-D7-6519        TCGA-D7-6520        TCGA-D7-6521        TCGA-D7-6522 
"6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" 
       TCGA-D7-6524        TCGA-D7-6525        TCGA-D7-6526        TCGA-D7-6527 
"6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" 
       TCGA-D7-6528        TCGA-D7-6815        TCGA-D7-6817        TCGA-D7-6818 
"6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" 
       TCGA-D7-6820        TCGA-D7-6822        TCGA-EQ-5647        TCGA-EQ-8122 
"6P GAIN WILD-TYPE"       "6P GAIN CNV" "6P GAIN WILD-TYPE"       "6P GAIN CNV" 
       TCGA-F1-6177        TCGA-F1-6874        TCGA-F1-6875        TCGA-FP-7735 
"6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" 
       TCGA-FP-7829        TCGA-FP-7916        TCGA-FP-7998        TCGA-FP-8099 
"6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" 
       TCGA-FP-8209        TCGA-FP-8210        TCGA-FP-8631        TCGA-HJ-7597 
"6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE"       "6P GAIN CNV" "6P GAIN WILD-TYPE" 
       TCGA-IN-7806        TCGA-IN-7808        TCGA-IP-7968 
"6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" 
[1] "hr=" "1.6"
D10V2, continuous
D10V3, binary
[1] "tbl2"
                   cls
clus                [,1] [,2]
  6P GAIN CNV          7   10
  6P GAIN WILD-TYPE   65   98
        clus
vv       6P GAIN CNV 6P GAIN WILD-TYPE
  FEMALE           7                65
  MALE            10                98
                   vv
clus                STOMACH  ADENOCARCINOMA  DIFFUSE TYPE
  6P GAIN CNV                                           0
  6P GAIN WILD-TYPE                                    10
                   vv
clus                STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  6P GAIN CNV                                                            1
  6P GAIN WILD-TYPE                                                     15
                   vv
clus                STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  6P GAIN CNV                                                                       2
  6P GAIN WILD-TYPE                                                                 6
                   vv
clus                STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE
  6P GAIN CNV                                                              0
  6P GAIN WILD-TYPE                                                        3
                   vv
clus                STOMACH ADENOCARCINOMA  SIGNET RING TYPE
  6P GAIN CNV                                              0
  6P GAIN WILD-TYPE                                        1
                   vv
clus                STOMACH ADENOCARCINOMA - DIFFUSE TYPE
  6P GAIN CNV                                           0
  6P GAIN WILD-TYPE                                    16
                   vv
clus                STOMACH ADENOCARCINOMA - NOT OTHERWISE SPECIFIED (NOS)
  6P GAIN CNV                                                            9
  6P GAIN WILD-TYPE                                                     64
                   vv
clus                STOMACH INTESTINAL ADENOCARCINOMA - MUCINOUS TYPE
  6P GAIN CNV                                                       0
  6P GAIN WILD-TYPE                                                 7
                   vv
clus                STOMACH INTESTINAL ADENOCARCINOMA - PAPILLARY TYPE
  6P GAIN CNV                                                        0
  6P GAIN WILD-TYPE                                                  3
                   vv
clus                STOMACH INTESTINAL ADENOCARCINOMA - TUBULAR TYPE
  6P GAIN CNV                                                      1
  6P GAIN WILD-TYPE                                                9
                   vv
clus                STOMACH INTESTINAL ADENOCARCINOMA - TYPE NOT OTHERWISE SPECIFIED (NOS)
  6P GAIN CNV                                                                            4
  6P GAIN WILD-TYPE                                                                     24
D10V4, multiclass
                   vv
clus                T1 T2 T3 T4
  6P GAIN CNV        1  2  6  4
  6P GAIN WILD-TYPE  5 50 50 14
D10V5, multiclass
    clus
vv   6P GAIN CNV 6P GAIN WILD-TYPE
  T1           1                 5
  T2           2                50
  T3           6                50
  T4           4                14
                   vv
clus                N0 N1 N2 N3
  6P GAIN CNV        6  5  3  0
  6P GAIN WILD-TYPE 38 44 20 15
D10V6, multiclass
    clus
vv   6P GAIN CNV 6P GAIN WILD-TYPE
  N0           6                38
  N1           5                44
  N2           3                20
  N3           0                15
                   vv
clus                 M0  M1  MX
  6P GAIN CNV        12   1   1
  6P GAIN WILD-TYPE 106  15   7
D10V7, multiclass
    clus
vv   6P GAIN CNV 6P GAIN WILD-TYPE
  M0          12               106
  M1           1                15
  MX           1                 7
                   vv
clus                 I II III IV
  6P GAIN CNV        3  4   2  4
  6P GAIN WILD-TYPE 21 33  37 22
D10V8, multiclass
     clus
vv    6P GAIN CNV 6P GAIN WILD-TYPE
  I             3                21
  II            4                33
  III           2                37
  IV            4                22
D10V9, binary
[1] "tbl2"
                   cls
clus                [,1] [,2]
  6P GAIN CNV          1   16
  6P GAIN WILD-TYPE    4  159
     clus
vv    6P GAIN CNV 6P GAIN WILD-TYPE
  NO            1                 4
  YES          16               159
                   vv
clus                 R0  R1  R2  RX
  6P GAIN CNV        11   1   1   3
  6P GAIN WILD-TYPE 114   6  11  22
D10V10, multiclass
    clus
vv   6P GAIN CNV 6P GAIN WILD-TYPE
  R0          11               114
  R1           1                 6
  R2           1                11
  RX           3                22
D10V11, continuous

Clustering(11) Variable = 6q gain
D11V1, survival
                   sevent
clus2                 0   1
  6Q GAIN CNV         9   0
  6Q GAIN WILD-TYPE 115  19
      6Q GAIN CNV 6Q GAIN WILD-TYPE 
                9               134 
      6Q GAIN CNV 6Q GAIN WILD-TYPE 
                0                19 
$`6Q GAIN CNV`
TCGA-BR-7197 TCGA-BR-7704 TCGA-BR-7715 TCGA-BR-7717 TCGA-BR-7723 TCGA-BR-8286 
        1.48         1.25         1.05         0.69         4.54         0.43 
TCGA-CG-4438 TCGA-D7-6822 TCGA-EQ-8122 
       54.05         4.27         7.79 

$`6Q GAIN WILD-TYPE`
TCGA-B7-5816 TCGA-B7-5818 TCGA-BR-6452 TCGA-BR-6455 TCGA-BR-6457 TCGA-BR-6458 
        5.62         0.10         0.95         1.41         1.35         1.35 
TCGA-BR-6563 TCGA-BR-6564 TCGA-BR-6565 TCGA-BR-6566 TCGA-BR-6705 TCGA-BR-6706 
        0.85         0.82         0.62         0.62         1.71         2.17 
TCGA-BR-6707 TCGA-BR-6709 TCGA-BR-6710 TCGA-BR-6801 TCGA-BR-6802 TCGA-BR-6803 
        0.99         1.22         0.66         1.12         0.76         0.66 
TCGA-BR-6852 TCGA-BR-7196 TCGA-BR-7703 TCGA-BR-7707 TCGA-BR-7716 TCGA-BR-7722 
        0.26         1.22         0.46         0.13         0.82         0.16 
TCGA-BR-7851 TCGA-BR-7901 TCGA-BR-7957 TCGA-BR-7958 TCGA-BR-7959 TCGA-BR-8059 
        0.99         0.95         0.69         0.16         1.08         0.82 
TCGA-BR-8060 TCGA-BR-8077 TCGA-BR-8078 TCGA-BR-8080 TCGA-BR-8081 TCGA-BR-8284 
        1.32         0.69         0.95         0.49         0.46         0.72 
TCGA-BR-8285 TCGA-BR-8289 TCGA-BR-8291 TCGA-BR-8295 TCGA-BR-8296 TCGA-BR-8297 
        0.26         0.26         1.18         1.55         1.48         0.76 
TCGA-BR-8592 TCGA-BR-A4IU TCGA-BR-A4IV TCGA-BR-A4IY TCGA-BR-A4IZ TCGA-BR-A4J1 
        0.20         0.59         0.92         0.39         0.79         0.72 
TCGA-BR-A4J2 TCGA-BR-A4J4 TCGA-BR-A4J5 TCGA-BR-A4J6 TCGA-BR-A4J8 TCGA-BR-A4J9 
        0.79         0.53         0.43         0.13         0.23         0.10 
TCGA-BR-A4PF TCGA-BR-A4QI TCGA-BR-A4QL TCGA-CD-5798 TCGA-CD-5799 TCGA-CD-5800 
        0.72         0.49         2.24         0.82         0.69         0.36 
TCGA-CD-5801 TCGA-CD-5802 TCGA-CD-5803 TCGA-CG-4300 TCGA-CG-4301 TCGA-CG-4304 
        0.49         0.30         0.07        20.02         3.02        27.02 
TCGA-CG-4305 TCGA-CG-4306 TCGA-CG-4436 TCGA-CG-4437 TCGA-CG-4440 TCGA-CG-4441 
       15.95         1.02        52.96         8.05         4.01        14.01 
TCGA-CG-4443 TCGA-CG-4444 TCGA-CG-4449 TCGA-CG-4455 TCGA-CG-4460 TCGA-CG-4462 
       29.98        47.05        19.07        12.03        21.99         1.02 
TCGA-CG-4465 TCGA-CG-4466 TCGA-CG-4469 TCGA-CG-4472 TCGA-CG-4474 TCGA-CG-4477 
        8.98        18.94         7.07        12.00         1.02         1.02 
TCGA-CG-5716 TCGA-CG-5717 TCGA-CG-5718 TCGA-CG-5719 TCGA-CG-5720 TCGA-CG-5721 
        1.02         6.94         1.02         1.02         0.99         5.98 
TCGA-CG-5722 TCGA-CG-5723 TCGA-CG-5724 TCGA-CG-5725 TCGA-CG-5726 TCGA-CG-5727 
        0.95        70.06        12.03        15.02        28.96        31.04 
TCGA-CG-5728 TCGA-CG-5730 TCGA-CG-5732 TCGA-CG-5733 TCGA-CG-5734 TCGA-D7-5577 
       65.10         4.01        55.04        21.07         7.99         8.65 
TCGA-D7-5578 TCGA-D7-5579 TCGA-D7-6518 TCGA-D7-6519 TCGA-D7-6520 TCGA-D7-6521 
        3.58         4.54         9.80        15.65         9.63         8.19 
TCGA-D7-6522 TCGA-D7-6524 TCGA-D7-6525 TCGA-D7-6526 TCGA-D7-6527 TCGA-D7-6528 
        6.90         0.69         5.95         6.61         4.14         1.68 
TCGA-D7-6815 TCGA-D7-6817 TCGA-D7-6818 TCGA-D7-6820 TCGA-EQ-5647 TCGA-F1-6177 
        3.65         4.70         4.04         2.93         0.62         6.54 
TCGA-F1-6874 TCGA-F1-6875 TCGA-FP-7735 TCGA-FP-7829 TCGA-FP-7916 TCGA-FP-7998 
        2.01        72.23         0.39         0.20         3.02         3.58 
TCGA-FP-8099 TCGA-FP-8209 TCGA-FP-8210 TCGA-FP-8631 TCGA-HJ-7597 TCGA-IN-7806 
        1.02        59.05         5.03         0.56        26.43         6.87 
TCGA-IN-7808 TCGA-IP-7968 
        3.55         2.53 

      6Q GAIN CNV 6Q GAIN WILD-TYPE 
             0.43              0.07 
      6Q GAIN CNV 6Q GAIN WILD-TYPE 
            54.05             72.23 
      6Q GAIN CNV 6Q GAIN WILD-TYPE 
             1.48              1.22 
[1] "0.4 - 54.0 (1.5)" "0.1 - 72.2 (1.2)"
       TCGA-B7-5816        TCGA-B7-5818        TCGA-BR-6452        TCGA-BR-6455 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" 
       TCGA-BR-6457        TCGA-BR-6458        TCGA-BR-6563        TCGA-BR-6564 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" 
       TCGA-BR-6565        TCGA-BR-6566        TCGA-BR-6705        TCGA-BR-6706 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" 
       TCGA-BR-6707        TCGA-BR-6709        TCGA-BR-6710        TCGA-BR-6801 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" 
       TCGA-BR-6802        TCGA-BR-6803        TCGA-BR-6852        TCGA-BR-7196 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" 
       TCGA-BR-7197        TCGA-BR-7703        TCGA-BR-7704        TCGA-BR-7707 
      "6Q GAIN CNV" "6Q GAIN WILD-TYPE"       "6Q GAIN CNV" "6Q GAIN WILD-TYPE" 
       TCGA-BR-7715        TCGA-BR-7716        TCGA-BR-7717        TCGA-BR-7722 
      "6Q GAIN CNV" "6Q GAIN WILD-TYPE"       "6Q GAIN CNV" "6Q GAIN WILD-TYPE" 
       TCGA-BR-7723        TCGA-BR-7851        TCGA-BR-7901        TCGA-BR-7957 
      "6Q GAIN CNV" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" 
       TCGA-BR-7958        TCGA-BR-7959        TCGA-BR-8059        TCGA-BR-8060 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" 
       TCGA-BR-8077        TCGA-BR-8078        TCGA-BR-8080        TCGA-BR-8081 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" 
       TCGA-BR-8284        TCGA-BR-8285        TCGA-BR-8286        TCGA-BR-8289 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE"       "6Q GAIN CNV" "6Q GAIN WILD-TYPE" 
       TCGA-BR-8291        TCGA-BR-8295        TCGA-BR-8296        TCGA-BR-8297 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" 
       TCGA-BR-8592        TCGA-BR-A4IU        TCGA-BR-A4IV        TCGA-BR-A4IY 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" 
       TCGA-BR-A4IZ        TCGA-BR-A4J1        TCGA-BR-A4J2        TCGA-BR-A4J4 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" 
       TCGA-BR-A4J5        TCGA-BR-A4J6        TCGA-BR-A4J8        TCGA-BR-A4J9 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" 
       TCGA-BR-A4PF        TCGA-BR-A4QI        TCGA-BR-A4QL        TCGA-CD-5798 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" 
       TCGA-CD-5799        TCGA-CD-5800        TCGA-CD-5801        TCGA-CD-5802 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" 
       TCGA-CD-5803        TCGA-CG-4300        TCGA-CG-4301        TCGA-CG-4304 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" 
       TCGA-CG-4305        TCGA-CG-4306        TCGA-CG-4436        TCGA-CG-4437 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" 
       TCGA-CG-4438        TCGA-CG-4440        TCGA-CG-4441        TCGA-CG-4443 
      "6Q GAIN CNV" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" 
       TCGA-CG-4444        TCGA-CG-4449        TCGA-CG-4455        TCGA-CG-4460 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" 
       TCGA-CG-4462        TCGA-CG-4465        TCGA-CG-4466        TCGA-CG-4469 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" 
       TCGA-CG-4472        TCGA-CG-4474        TCGA-CG-4477        TCGA-CG-5716 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" 
       TCGA-CG-5717        TCGA-CG-5718        TCGA-CG-5719        TCGA-CG-5720 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" 
       TCGA-CG-5721        TCGA-CG-5722        TCGA-CG-5723        TCGA-CG-5724 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" 
       TCGA-CG-5725        TCGA-CG-5726        TCGA-CG-5727        TCGA-CG-5728 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" 
       TCGA-CG-5730        TCGA-CG-5732        TCGA-CG-5733        TCGA-CG-5734 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" 
       TCGA-D7-5577        TCGA-D7-5578        TCGA-D7-5579        TCGA-D7-6518 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" 
       TCGA-D7-6519        TCGA-D7-6520        TCGA-D7-6521        TCGA-D7-6522 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" 
       TCGA-D7-6524        TCGA-D7-6525        TCGA-D7-6526        TCGA-D7-6527 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" 
       TCGA-D7-6528        TCGA-D7-6815        TCGA-D7-6817        TCGA-D7-6818 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" 
       TCGA-D7-6820        TCGA-D7-6822        TCGA-EQ-5647        TCGA-EQ-8122 
"6Q GAIN WILD-TYPE"       "6Q GAIN CNV" "6Q GAIN WILD-TYPE"       "6Q GAIN CNV" 
       TCGA-F1-6177        TCGA-F1-6874        TCGA-F1-6875        TCGA-FP-7735 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" 
       TCGA-FP-7829        TCGA-FP-7916        TCGA-FP-7998        TCGA-FP-8099 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" 
       TCGA-FP-8209        TCGA-FP-8210        TCGA-FP-8631        TCGA-HJ-7597 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" 
       TCGA-IN-7806        TCGA-IN-7808        TCGA-IP-7968 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" 
       TCGA-B7-5816        TCGA-B7-5818        TCGA-BR-6452        TCGA-BR-6455 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" 
       TCGA-BR-6457        TCGA-BR-6458        TCGA-BR-6563        TCGA-BR-6564 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" 
       TCGA-BR-6565        TCGA-BR-6566        TCGA-BR-6705        TCGA-BR-6706 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" 
       TCGA-BR-6707        TCGA-BR-6709        TCGA-BR-6710        TCGA-BR-6801 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" 
       TCGA-BR-6802        TCGA-BR-6803        TCGA-BR-6852        TCGA-BR-7196 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" 
       TCGA-BR-7197        TCGA-BR-7703        TCGA-BR-7704        TCGA-BR-7707 
      "6Q GAIN CNV" "6Q GAIN WILD-TYPE"       "6Q GAIN CNV" "6Q GAIN WILD-TYPE" 
       TCGA-BR-7715        TCGA-BR-7716        TCGA-BR-7717        TCGA-BR-7722 
      "6Q GAIN CNV" "6Q GAIN WILD-TYPE"       "6Q GAIN CNV" "6Q GAIN WILD-TYPE" 
       TCGA-BR-7723        TCGA-BR-7851        TCGA-BR-7901        TCGA-BR-7957 
      "6Q GAIN CNV" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" 
       TCGA-BR-7958        TCGA-BR-7959        TCGA-BR-8059        TCGA-BR-8060 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" 
       TCGA-BR-8077        TCGA-BR-8078        TCGA-BR-8080        TCGA-BR-8081 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" 
       TCGA-BR-8284        TCGA-BR-8285        TCGA-BR-8286        TCGA-BR-8289 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE"       "6Q GAIN CNV" "6Q GAIN WILD-TYPE" 
       TCGA-BR-8291        TCGA-BR-8295        TCGA-BR-8296        TCGA-BR-8297 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" 
       TCGA-BR-8592        TCGA-BR-A4IU        TCGA-BR-A4IV        TCGA-BR-A4IY 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" 
       TCGA-BR-A4IZ        TCGA-BR-A4J1        TCGA-BR-A4J2        TCGA-BR-A4J4 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" 
       TCGA-BR-A4J5        TCGA-BR-A4J6        TCGA-BR-A4J8        TCGA-BR-A4J9 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" 
       TCGA-BR-A4PF        TCGA-BR-A4QI        TCGA-BR-A4QL        TCGA-CD-5798 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" 
       TCGA-CD-5799        TCGA-CD-5800        TCGA-CD-5801        TCGA-CD-5802 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" 
       TCGA-CD-5803        TCGA-CG-4300        TCGA-CG-4301        TCGA-CG-4304 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" 
       TCGA-CG-4305        TCGA-CG-4306        TCGA-CG-4436        TCGA-CG-4437 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" 
       TCGA-CG-4438        TCGA-CG-4440        TCGA-CG-4441        TCGA-CG-4443 
      "6Q GAIN CNV" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" 
       TCGA-CG-4444        TCGA-CG-4449        TCGA-CG-4455        TCGA-CG-4460 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" 
       TCGA-CG-4462        TCGA-CG-4465        TCGA-CG-4466        TCGA-CG-4469 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" 
       TCGA-CG-4472        TCGA-CG-4474        TCGA-CG-4477        TCGA-CG-5716 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" 
       TCGA-CG-5717        TCGA-CG-5718        TCGA-CG-5719        TCGA-CG-5720 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" 
       TCGA-CG-5721        TCGA-CG-5722        TCGA-CG-5723        TCGA-CG-5724 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" 
       TCGA-CG-5725        TCGA-CG-5726        TCGA-CG-5727        TCGA-CG-5728 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" 
       TCGA-CG-5730        TCGA-CG-5732        TCGA-CG-5733        TCGA-CG-5734 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" 
       TCGA-D7-5577        TCGA-D7-5578        TCGA-D7-5579        TCGA-D7-6518 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" 
       TCGA-D7-6519        TCGA-D7-6520        TCGA-D7-6521        TCGA-D7-6522 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" 
       TCGA-D7-6524        TCGA-D7-6525        TCGA-D7-6526        TCGA-D7-6527 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" 
       TCGA-D7-6528        TCGA-D7-6815        TCGA-D7-6817        TCGA-D7-6818 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" 
       TCGA-D7-6820        TCGA-D7-6822        TCGA-EQ-5647        TCGA-EQ-8122 
"6Q GAIN WILD-TYPE"       "6Q GAIN CNV" "6Q GAIN WILD-TYPE"       "6Q GAIN CNV" 
       TCGA-F1-6177        TCGA-F1-6874        TCGA-F1-6875        TCGA-FP-7735 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" 
       TCGA-FP-7829        TCGA-FP-7916        TCGA-FP-7998        TCGA-FP-8099 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" 
       TCGA-FP-8209        TCGA-FP-8210        TCGA-FP-8631        TCGA-HJ-7597 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" 
       TCGA-IN-7806        TCGA-IN-7808        TCGA-IP-7968 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" 
       TCGA-B7-5816        TCGA-B7-5818        TCGA-BR-6452        TCGA-BR-6455 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" 
       TCGA-BR-6457        TCGA-BR-6458        TCGA-BR-6563        TCGA-BR-6564 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" 
       TCGA-BR-6565        TCGA-BR-6566        TCGA-BR-6705        TCGA-BR-6706 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" 
       TCGA-BR-6707        TCGA-BR-6709        TCGA-BR-6710        TCGA-BR-6801 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" 
       TCGA-BR-6802        TCGA-BR-6803        TCGA-BR-6852        TCGA-BR-7196 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" 
       TCGA-BR-7197        TCGA-BR-7703        TCGA-BR-7704        TCGA-BR-7707 
      "6Q GAIN CNV" "6Q GAIN WILD-TYPE"       "6Q GAIN CNV" "6Q GAIN WILD-TYPE" 
       TCGA-BR-7715        TCGA-BR-7716        TCGA-BR-7717        TCGA-BR-7722 
      "6Q GAIN CNV" "6Q GAIN WILD-TYPE"       "6Q GAIN CNV" "6Q GAIN WILD-TYPE" 
       TCGA-BR-7723        TCGA-BR-7851        TCGA-BR-7901        TCGA-BR-7957 
      "6Q GAIN CNV" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" 
       TCGA-BR-7958        TCGA-BR-7959        TCGA-BR-8059        TCGA-BR-8060 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" 
       TCGA-BR-8077        TCGA-BR-8078        TCGA-BR-8080        TCGA-BR-8081 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" 
       TCGA-BR-8284        TCGA-BR-8285        TCGA-BR-8286        TCGA-BR-8289 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE"       "6Q GAIN CNV" "6Q GAIN WILD-TYPE" 
       TCGA-BR-8291        TCGA-BR-8295        TCGA-BR-8296        TCGA-BR-8297 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" 
       TCGA-BR-8592        TCGA-BR-A4IU        TCGA-BR-A4IV        TCGA-BR-A4IY 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" 
       TCGA-BR-A4IZ        TCGA-BR-A4J1        TCGA-BR-A4J2        TCGA-BR-A4J4 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" 
       TCGA-BR-A4J5        TCGA-BR-A4J6        TCGA-BR-A4J8        TCGA-BR-A4J9 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" 
       TCGA-BR-A4PF        TCGA-BR-A4QI        TCGA-BR-A4QL        TCGA-CD-5798 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" 
       TCGA-CD-5799        TCGA-CD-5800        TCGA-CD-5801        TCGA-CD-5802 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" 
       TCGA-CD-5803        TCGA-CG-4300        TCGA-CG-4301        TCGA-CG-4304 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" 
       TCGA-CG-4305        TCGA-CG-4306        TCGA-CG-4436        TCGA-CG-4437 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" 
       TCGA-CG-4438        TCGA-CG-4440        TCGA-CG-4441        TCGA-CG-4443 
      "6Q GAIN CNV" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" 
       TCGA-CG-4444        TCGA-CG-4449        TCGA-CG-4455        TCGA-CG-4460 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" 
       TCGA-CG-4462        TCGA-CG-4465        TCGA-CG-4466        TCGA-CG-4469 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" 
       TCGA-CG-4472        TCGA-CG-4474        TCGA-CG-4477        TCGA-CG-5716 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" 
       TCGA-CG-5717        TCGA-CG-5718        TCGA-CG-5719        TCGA-CG-5720 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" 
       TCGA-CG-5721        TCGA-CG-5722        TCGA-CG-5723        TCGA-CG-5724 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" 
       TCGA-CG-5725        TCGA-CG-5726        TCGA-CG-5727        TCGA-CG-5728 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" 
       TCGA-CG-5730        TCGA-CG-5732        TCGA-CG-5733        TCGA-CG-5734 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" 
       TCGA-D7-5577        TCGA-D7-5578        TCGA-D7-5579        TCGA-D7-6518 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" 
       TCGA-D7-6519        TCGA-D7-6520        TCGA-D7-6521        TCGA-D7-6522 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" 
       TCGA-D7-6524        TCGA-D7-6525        TCGA-D7-6526        TCGA-D7-6527 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" 
       TCGA-D7-6528        TCGA-D7-6815        TCGA-D7-6817        TCGA-D7-6818 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" 
       TCGA-D7-6820        TCGA-D7-6822        TCGA-EQ-5647        TCGA-EQ-8122 
"6Q GAIN WILD-TYPE"       "6Q GAIN CNV" "6Q GAIN WILD-TYPE"       "6Q GAIN CNV" 
       TCGA-F1-6177        TCGA-F1-6874        TCGA-F1-6875        TCGA-FP-7735 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" 
       TCGA-FP-7829        TCGA-FP-7916        TCGA-FP-7998        TCGA-FP-8099 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" 
       TCGA-FP-8209        TCGA-FP-8210        TCGA-FP-8631        TCGA-HJ-7597 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" 
       TCGA-IN-7806        TCGA-IN-7808        TCGA-IP-7968 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" 
[1] "hr="     "7.3e+07"
D11V2, continuous
D11V3, binary
[1] "tbl2"
                   cls
clus                [,1] [,2]
  6Q GAIN CNV          6    8
  6Q GAIN WILD-TYPE   66  100
        clus
vv       6Q GAIN CNV 6Q GAIN WILD-TYPE
  FEMALE           6                66
  MALE             8               100
                   vv
clus                STOMACH  ADENOCARCINOMA  DIFFUSE TYPE
  6Q GAIN CNV                                           0
  6Q GAIN WILD-TYPE                                    10
                   vv
clus                STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  6Q GAIN CNV                                                            1
  6Q GAIN WILD-TYPE                                                     15
                   vv
clus                STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  6Q GAIN CNV                                                                       1
  6Q GAIN WILD-TYPE                                                                 7
                   vv
clus                STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE
  6Q GAIN CNV                                                              0
  6Q GAIN WILD-TYPE                                                        3
                   vv
clus                STOMACH ADENOCARCINOMA  SIGNET RING TYPE
  6Q GAIN CNV                                              0
  6Q GAIN WILD-TYPE                                        1
                   vv
clus                STOMACH ADENOCARCINOMA - DIFFUSE TYPE
  6Q GAIN CNV                                           0
  6Q GAIN WILD-TYPE                                    16
                   vv
clus                STOMACH ADENOCARCINOMA - NOT OTHERWISE SPECIFIED (NOS)
  6Q GAIN CNV                                                            9
  6Q GAIN WILD-TYPE                                                     64
                   vv
clus                STOMACH INTESTINAL ADENOCARCINOMA - MUCINOUS TYPE
  6Q GAIN CNV                                                       0
  6Q GAIN WILD-TYPE                                                 7
                   vv
clus                STOMACH INTESTINAL ADENOCARCINOMA - PAPILLARY TYPE
  6Q GAIN CNV                                                        0
  6Q GAIN WILD-TYPE                                                  3
                   vv
clus                STOMACH INTESTINAL ADENOCARCINOMA - TUBULAR TYPE
  6Q GAIN CNV                                                      1
  6Q GAIN WILD-TYPE                                                9
                   vv
clus                STOMACH INTESTINAL ADENOCARCINOMA - TYPE NOT OTHERWISE SPECIFIED (NOS)
  6Q GAIN CNV                                                                            2
  6Q GAIN WILD-TYPE                                                                     26
D11V4, multiclass
                   vv
clus                T1 T2 T3 T4
  6Q GAIN CNV        0  2  6  3
  6Q GAIN WILD-TYPE  6 50 50 15
D11V5, multiclass
    clus
vv   6Q GAIN CNV 6Q GAIN WILD-TYPE
  T1           0                 6
  T2           2                50
  T3           6                50
  T4           3                15
                   vv
clus                N0 N1 N2 N3
  6Q GAIN CNV        5  4  3  0
  6Q GAIN WILD-TYPE 39 45 20 15
D11V6, multiclass
    clus
vv   6Q GAIN CNV 6Q GAIN WILD-TYPE
  N0           5                39
  N1           4                45
  N2           3                20
  N3           0                15
                   vv
clus                 M0  M1  MX
  6Q GAIN CNV        11   0   1
  6Q GAIN WILD-TYPE 107  16   7
D11V7, multiclass
    clus
vv   6Q GAIN CNV 6Q GAIN WILD-TYPE
  M0          11               107
  M1           0                16
  MX           1                 7
                   vv
clus                 I II III IV
  6Q GAIN CNV        2  4   2  3
  6Q GAIN WILD-TYPE 22 33  37 23
D11V8, multiclass
     clus
vv    6Q GAIN CNV 6Q GAIN WILD-TYPE
  I             2                22
  II            4                33
  III           2                37
  IV            3                23
D11V9, binary
[1] "tbl2"
                   cls
clus                [,1] [,2]
  6Q GAIN CNV          1   13
  6Q GAIN WILD-TYPE    4  162
     clus
vv    6Q GAIN CNV 6Q GAIN WILD-TYPE
  NO            1                 4
  YES          13               162
                   vv
clus                 R0  R1  R2  RX
  6Q GAIN CNV         9   1   0   3
  6Q GAIN WILD-TYPE 116   6  12  22
D11V10, multiclass
    clus
vv   6Q GAIN CNV 6Q GAIN WILD-TYPE
  R0           9               116
  R1           1                 6
  R2           0                12
  RX           3                22
D11V11, continuous

Clustering(12) Variable = 7p gain
D12V1, survival
                   sevent
clus2                0  1
  7P GAIN CNV       39  6
  7P GAIN WILD-TYPE 85 13
      7P GAIN CNV 7P GAIN WILD-TYPE 
               45                98 
      7P GAIN CNV 7P GAIN WILD-TYPE 
                6                13 
$`7P GAIN CNV`
TCGA-B7-5818 TCGA-BR-6565 TCGA-BR-6566 TCGA-BR-6801 TCGA-BR-7197 TCGA-BR-7704 
        0.10         0.62         0.62         1.12         1.48         1.25 
TCGA-BR-7715 TCGA-BR-7717 TCGA-BR-7901 TCGA-BR-7958 TCGA-BR-8077 TCGA-BR-8284 
        1.05         0.69         0.95         0.16         0.69         0.72 
TCGA-BR-8285 TCGA-BR-8286 TCGA-BR-8295 TCGA-BR-A4IY TCGA-BR-A4J4 TCGA-BR-A4J8 
        0.26         0.43         1.55         0.39         0.53         0.23 
TCGA-BR-A4QI TCGA-CD-5801 TCGA-CG-4300 TCGA-CG-4304 TCGA-CG-4305 TCGA-CG-4436 
        0.49         0.49        20.02        27.02        15.95        52.96 
TCGA-CG-4460 TCGA-CG-4469 TCGA-CG-4472 TCGA-CG-4474 TCGA-CG-5718 TCGA-CG-5724 
       21.99         7.07        12.00         1.02         1.02        12.03 
TCGA-CG-5726 TCGA-CG-5727 TCGA-CG-5733 TCGA-D7-6518 TCGA-D7-6521 TCGA-D7-6526 
       28.96        31.04        21.07         9.80         8.19         6.61 
TCGA-D7-6528 TCGA-D7-6818 TCGA-D7-6822 TCGA-F1-6177 TCGA-F1-6874 TCGA-F1-6875 
        1.68         4.04         4.27         6.54         2.01        72.23 
TCGA-FP-7735 TCGA-FP-8099 TCGA-IN-7808 
        0.39         1.02         3.55 

$`7P GAIN WILD-TYPE`
TCGA-B7-5816 TCGA-BR-6452 TCGA-BR-6455 TCGA-BR-6457 TCGA-BR-6458 TCGA-BR-6563 
        5.62         0.95         1.41         1.35         1.35         0.85 
TCGA-BR-6564 TCGA-BR-6705 TCGA-BR-6706 TCGA-BR-6707 TCGA-BR-6709 TCGA-BR-6710 
        0.82         1.71         2.17         0.99         1.22         0.66 
TCGA-BR-6802 TCGA-BR-6803 TCGA-BR-6852 TCGA-BR-7196 TCGA-BR-7703 TCGA-BR-7707 
        0.76         0.66         0.26         1.22         0.46         0.13 
TCGA-BR-7716 TCGA-BR-7722 TCGA-BR-7723 TCGA-BR-7851 TCGA-BR-7957 TCGA-BR-7959 
        0.82         0.16         4.54         0.99         0.69         1.08 
TCGA-BR-8059 TCGA-BR-8060 TCGA-BR-8078 TCGA-BR-8080 TCGA-BR-8081 TCGA-BR-8289 
        0.82         1.32         0.95         0.49         0.46         0.26 
TCGA-BR-8291 TCGA-BR-8296 TCGA-BR-8297 TCGA-BR-8592 TCGA-BR-A4IU TCGA-BR-A4IV 
        1.18         1.48         0.76         0.20         0.59         0.92 
TCGA-BR-A4IZ TCGA-BR-A4J1 TCGA-BR-A4J2 TCGA-BR-A4J5 TCGA-BR-A4J6 TCGA-BR-A4J9 
        0.79         0.72         0.79         0.43         0.13         0.10 
TCGA-BR-A4PF TCGA-BR-A4QL TCGA-CD-5798 TCGA-CD-5799 TCGA-CD-5800 TCGA-CD-5802 
        0.72         2.24         0.82         0.69         0.36         0.30 
TCGA-CD-5803 TCGA-CG-4301 TCGA-CG-4306 TCGA-CG-4437 TCGA-CG-4438 TCGA-CG-4440 
        0.07         3.02         1.02         8.05        54.05         4.01 
TCGA-CG-4441 TCGA-CG-4443 TCGA-CG-4444 TCGA-CG-4449 TCGA-CG-4455 TCGA-CG-4462 
       14.01        29.98        47.05        19.07        12.03         1.02 
TCGA-CG-4465 TCGA-CG-4466 TCGA-CG-4477 TCGA-CG-5716 TCGA-CG-5717 TCGA-CG-5719 
        8.98        18.94         1.02         1.02         6.94         1.02 
TCGA-CG-5720 TCGA-CG-5721 TCGA-CG-5722 TCGA-CG-5723 TCGA-CG-5725 TCGA-CG-5728 
        0.99         5.98         0.95        70.06        15.02        65.10 
TCGA-CG-5730 TCGA-CG-5732 TCGA-CG-5734 TCGA-D7-5577 TCGA-D7-5578 TCGA-D7-5579 
        4.01        55.04         7.99         8.65         3.58         4.54 
TCGA-D7-6519 TCGA-D7-6520 TCGA-D7-6522 TCGA-D7-6524 TCGA-D7-6525 TCGA-D7-6527 
       15.65         9.63         6.90         0.69         5.95         4.14 
TCGA-D7-6815 TCGA-D7-6817 TCGA-D7-6820 TCGA-EQ-5647 TCGA-EQ-8122 TCGA-FP-7829 
        3.65         4.70         2.93         0.62         7.79         0.20 
TCGA-FP-7916 TCGA-FP-7998 TCGA-FP-8209 TCGA-FP-8210 TCGA-FP-8631 TCGA-HJ-7597 
        3.02         3.58        59.05         5.03         0.56        26.43 
TCGA-IN-7806 TCGA-IP-7968 
        6.87         2.53 

      7P GAIN CNV 7P GAIN WILD-TYPE 
             0.10              0.07 
      7P GAIN CNV 7P GAIN WILD-TYPE 
            72.23             70.06 
      7P GAIN CNV 7P GAIN WILD-TYPE 
             1.48              1.22 
[1] "0.1 - 72.2 (1.5)" "0.1 - 70.1 (1.2)"
       TCGA-B7-5816        TCGA-B7-5818        TCGA-BR-6452        TCGA-BR-6455 
"7P GAIN WILD-TYPE"       "7P GAIN CNV" "7P GAIN WILD-TYPE" "7P GAIN WILD-TYPE" 
       TCGA-BR-6457        TCGA-BR-6458        TCGA-BR-6563        TCGA-BR-6564 
"7P GAIN WILD-TYPE" "7P GAIN WILD-TYPE" "7P GAIN WILD-TYPE" "7P GAIN WILD-TYPE" 
       TCGA-BR-6565        TCGA-BR-6566        TCGA-BR-6705        TCGA-BR-6706 
      "7P GAIN CNV"       "7P GAIN CNV" "7P GAIN WILD-TYPE" "7P GAIN WILD-TYPE" 
       TCGA-BR-6707        TCGA-BR-6709        TCGA-BR-6710        TCGA-BR-6801 
"7P GAIN WILD-TYPE" "7P GAIN WILD-TYPE" "7P GAIN WILD-TYPE"       "7P GAIN CNV" 
       TCGA-BR-6802        TCGA-BR-6803        TCGA-BR-6852        TCGA-BR-7196 
"7P GAIN WILD-TYPE" "7P GAIN WILD-TYPE" "7P GAIN WILD-TYPE" "7P GAIN WILD-TYPE" 
       TCGA-BR-7197        TCGA-BR-7703        TCGA-BR-7704        TCGA-BR-7707 
      "7P GAIN CNV" "7P GAIN WILD-TYPE"       "7P GAIN CNV" "7P GAIN WILD-TYPE" 
       TCGA-BR-7715        TCGA-BR-7716        TCGA-BR-7717        TCGA-BR-7722 
      "7P GAIN CNV" "7P GAIN WILD-TYPE"       "7P GAIN CNV" "7P GAIN WILD-TYPE" 
       TCGA-BR-7723        TCGA-BR-7851        TCGA-BR-7901        TCGA-BR-7957 
"7P GAIN WILD-TYPE" "7P GAIN WILD-TYPE"       "7P GAIN CNV" "7P GAIN WILD-TYPE" 
       TCGA-BR-7958        TCGA-BR-7959        TCGA-BR-8059        TCGA-BR-8060 
      "7P GAIN CNV" "7P GAIN WILD-TYPE" "7P GAIN WILD-TYPE" "7P GAIN WILD-TYPE" 
       TCGA-BR-8077        TCGA-BR-8078        TCGA-BR-8080        TCGA-BR-8081 
      "7P GAIN CNV" "7P GAIN WILD-TYPE" "7P GAIN WILD-TYPE" "7P GAIN WILD-TYPE" 
       TCGA-BR-8284        TCGA-BR-8285        TCGA-BR-8286        TCGA-BR-8289 
      "7P GAIN CNV"       "7P GAIN CNV"       "7P GAIN CNV" "7P GAIN WILD-TYPE" 
       TCGA-BR-8291        TCGA-BR-8295        TCGA-BR-8296        TCGA-BR-8297 
"7P GAIN WILD-TYPE"       "7P GAIN CNV" "7P GAIN WILD-TYPE" "7P GAIN WILD-TYPE" 
       TCGA-BR-8592        TCGA-BR-A4IU        TCGA-BR-A4IV        TCGA-BR-A4IY 
"7P GAIN WILD-TYPE" "7P GAIN WILD-TYPE" "7P GAIN WILD-TYPE"       "7P GAIN CNV" 
       TCGA-BR-A4IZ        TCGA-BR-A4J1        TCGA-BR-A4J2        TCGA-BR-A4J4 
"7P GAIN WILD-TYPE" "7P GAIN WILD-TYPE" "7P GAIN WILD-TYPE"       "7P GAIN CNV" 
       TCGA-BR-A4J5        TCGA-BR-A4J6        TCGA-BR-A4J8        TCGA-BR-A4J9 
"7P GAIN WILD-TYPE" "7P GAIN WILD-TYPE"       "7P GAIN CNV" "7P GAIN WILD-TYPE" 
       TCGA-BR-A4PF        TCGA-BR-A4QI        TCGA-BR-A4QL        TCGA-CD-5798 
"7P GAIN WILD-TYPE"       "7P GAIN CNV" "7P GAIN WILD-TYPE" "7P GAIN WILD-TYPE" 
       TCGA-CD-5799        TCGA-CD-5800        TCGA-CD-5801        TCGA-CD-5802 
"7P GAIN WILD-TYPE" "7P GAIN WILD-TYPE"       "7P GAIN CNV" "7P GAIN WILD-TYPE" 
       TCGA-CD-5803        TCGA-CG-4300        TCGA-CG-4301        TCGA-CG-4304 
"7P GAIN WILD-TYPE"       "7P GAIN CNV" "7P GAIN WILD-TYPE"       "7P GAIN CNV" 
       TCGA-CG-4305        TCGA-CG-4306        TCGA-CG-4436        TCGA-CG-4437 
      "7P GAIN CNV" "7P GAIN WILD-TYPE"       "7P GAIN CNV" "7P GAIN WILD-TYPE" 
       TCGA-CG-4438        TCGA-CG-4440        TCGA-CG-4441        TCGA-CG-4443 
"7P GAIN WILD-TYPE" "7P GAIN WILD-TYPE" "7P GAIN WILD-TYPE" "7P GAIN WILD-TYPE" 
       TCGA-CG-4444        TCGA-CG-4449        TCGA-CG-4455        TCGA-CG-4460 
"7P GAIN WILD-TYPE" "7P GAIN WILD-TYPE" "7P GAIN WILD-TYPE"       "7P GAIN CNV" 
       TCGA-CG-4462        TCGA-CG-4465        TCGA-CG-4466        TCGA-CG-4469 
"7P GAIN WILD-TYPE" "7P GAIN WILD-TYPE" "7P GAIN WILD-TYPE"       "7P GAIN CNV" 
       TCGA-CG-4472        TCGA-CG-4474        TCGA-CG-4477        TCGA-CG-5716 
      "7P GAIN CNV"       "7P GAIN CNV" "7P GAIN WILD-TYPE" "7P GAIN WILD-TYPE" 
       TCGA-CG-5717        TCGA-CG-5718        TCGA-CG-5719        TCGA-CG-5720 
"7P GAIN WILD-TYPE"       "7P GAIN CNV" "7P GAIN WILD-TYPE" "7P GAIN WILD-TYPE" 
       TCGA-CG-5721        TCGA-CG-5722        TCGA-CG-5723        TCGA-CG-5724 
"7P GAIN WILD-TYPE" "7P GAIN WILD-TYPE" "7P GAIN WILD-TYPE"       "7P GAIN CNV" 
       TCGA-CG-5725        TCGA-CG-5726        TCGA-CG-5727        TCGA-CG-5728 
"7P GAIN WILD-TYPE"       "7P GAIN CNV"       "7P GAIN CNV" "7P GAIN WILD-TYPE" 
       TCGA-CG-5730        TCGA-CG-5732        TCGA-CG-5733        TCGA-CG-5734 
"7P GAIN WILD-TYPE" "7P GAIN WILD-TYPE"       "7P GAIN CNV" "7P GAIN WILD-TYPE" 
       TCGA-D7-5577        TCGA-D7-5578        TCGA-D7-5579        TCGA-D7-6518 
"7P GAIN WILD-TYPE" "7P GAIN WILD-TYPE" "7P GAIN WILD-TYPE"       "7P GAIN CNV" 
       TCGA-D7-6519        TCGA-D7-6520        TCGA-D7-6521        TCGA-D7-6522 
"7P GAIN WILD-TYPE" "7P GAIN WILD-TYPE"       "7P GAIN CNV" "7P GAIN WILD-TYPE" 
       TCGA-D7-6524        TCGA-D7-6525        TCGA-D7-6526        TCGA-D7-6527 
"7P GAIN WILD-TYPE" "7P GAIN WILD-TYPE"       "7P GAIN CNV" "7P GAIN WILD-TYPE" 
       TCGA-D7-6528        TCGA-D7-6815        TCGA-D7-6817        TCGA-D7-6818 
      "7P GAIN CNV" "7P GAIN WILD-TYPE" "7P GAIN WILD-TYPE"       "7P GAIN CNV" 
       TCGA-D7-6820        TCGA-D7-6822        TCGA-EQ-5647        TCGA-EQ-8122 
"7P GAIN WILD-TYPE"       "7P GAIN CNV" "7P GAIN WILD-TYPE" "7P GAIN WILD-TYPE" 
       TCGA-F1-6177        TCGA-F1-6874        TCGA-F1-6875        TCGA-FP-7735 
      "7P GAIN CNV"       "7P GAIN CNV"       "7P GAIN CNV"       "7P GAIN CNV" 
       TCGA-FP-7829        TCGA-FP-7916        TCGA-FP-7998        TCGA-FP-8099 
"7P GAIN WILD-TYPE" "7P GAIN WILD-TYPE" "7P GAIN WILD-TYPE"       "7P GAIN CNV" 
       TCGA-FP-8209        TCGA-FP-8210        TCGA-FP-8631        TCGA-HJ-7597 
"7P GAIN WILD-TYPE" "7P GAIN WILD-TYPE" "7P GAIN WILD-TYPE" "7P GAIN WILD-TYPE" 
       TCGA-IN-7806        TCGA-IN-7808        TCGA-IP-7968 
"7P GAIN WILD-TYPE"       "7P GAIN CNV" "7P GAIN WILD-TYPE" 
       TCGA-B7-5816        TCGA-B7-5818        TCGA-BR-6452        TCGA-BR-6455 
"7P GAIN WILD-TYPE"       "7P GAIN CNV" "7P GAIN WILD-TYPE" "7P GAIN WILD-TYPE" 
       TCGA-BR-6457        TCGA-BR-6458        TCGA-BR-6563        TCGA-BR-6564 
"7P GAIN WILD-TYPE" "7P GAIN WILD-TYPE" "7P GAIN WILD-TYPE" "7P GAIN WILD-TYPE" 
       TCGA-BR-6565        TCGA-BR-6566        TCGA-BR-6705        TCGA-BR-6706 
      "7P GAIN CNV"       "7P GAIN CNV" "7P GAIN WILD-TYPE" "7P GAIN WILD-TYPE" 
       TCGA-BR-6707        TCGA-BR-6709        TCGA-BR-6710        TCGA-BR-6801 
"7P GAIN WILD-TYPE" "7P GAIN WILD-TYPE" "7P GAIN WILD-TYPE"       "7P GAIN CNV" 
       TCGA-BR-6802        TCGA-BR-6803        TCGA-BR-6852        TCGA-BR-7196 
"7P GAIN WILD-TYPE" "7P GAIN WILD-TYPE" "7P GAIN WILD-TYPE" "7P GAIN WILD-TYPE" 
       TCGA-BR-7197        TCGA-BR-7703        TCGA-BR-7704        TCGA-BR-7707 
      "7P GAIN CNV" "7P GAIN WILD-TYPE"       "7P GAIN CNV" "7P GAIN WILD-TYPE" 
       TCGA-BR-7715        TCGA-BR-7716        TCGA-BR-7717        TCGA-BR-7722 
      "7P GAIN CNV" "7P GAIN WILD-TYPE"       "7P GAIN CNV" "7P GAIN WILD-TYPE" 
       TCGA-BR-7723        TCGA-BR-7851        TCGA-BR-7901        TCGA-BR-7957 
"7P GAIN WILD-TYPE" "7P GAIN WILD-TYPE"       "7P GAIN CNV" "7P GAIN WILD-TYPE" 
       TCGA-BR-7958        TCGA-BR-7959        TCGA-BR-8059        TCGA-BR-8060 
      "7P GAIN CNV" "7P GAIN WILD-TYPE" "7P GAIN WILD-TYPE" "7P GAIN WILD-TYPE" 
       TCGA-BR-8077        TCGA-BR-8078        TCGA-BR-8080        TCGA-BR-8081 
      "7P GAIN CNV" "7P GAIN WILD-TYPE" "7P GAIN WILD-TYPE" "7P GAIN WILD-TYPE" 
       TCGA-BR-8284        TCGA-BR-8285        TCGA-BR-8286        TCGA-BR-8289 
      "7P GAIN CNV"       "7P GAIN CNV"       "7P GAIN CNV" "7P GAIN WILD-TYPE" 
       TCGA-BR-8291        TCGA-BR-8295        TCGA-BR-8296        TCGA-BR-8297 
"7P GAIN WILD-TYPE"       "7P GAIN CNV" "7P GAIN WILD-TYPE" "7P GAIN WILD-TYPE" 
       TCGA-BR-8592        TCGA-BR-A4IU        TCGA-BR-A4IV        TCGA-BR-A4IY 
"7P GAIN WILD-TYPE" "7P GAIN WILD-TYPE" "7P GAIN WILD-TYPE"       "7P GAIN CNV" 
       TCGA-BR-A4IZ        TCGA-BR-A4J1        TCGA-BR-A4J2        TCGA-BR-A4J4 
"7P GAIN WILD-TYPE" "7P GAIN WILD-TYPE" "7P GAIN WILD-TYPE"       "7P GAIN CNV" 
       TCGA-BR-A4J5        TCGA-BR-A4J6        TCGA-BR-A4J8        TCGA-BR-A4J9 
"7P GAIN WILD-TYPE" "7P GAIN WILD-TYPE"       "7P GAIN CNV" "7P GAIN WILD-TYPE" 
       TCGA-BR-A4PF        TCGA-BR-A4QI        TCGA-BR-A4QL        TCGA-CD-5798 
"7P GAIN WILD-TYPE"       "7P GAIN CNV" "7P GAIN WILD-TYPE" "7P GAIN WILD-TYPE" 
       TCGA-CD-5799        TCGA-CD-5800        TCGA-CD-5801        TCGA-CD-5802 
"7P GAIN WILD-TYPE" "7P GAIN WILD-TYPE"       "7P GAIN CNV" "7P GAIN WILD-TYPE" 
       TCGA-CD-5803        TCGA-CG-4300        TCGA-CG-4301        TCGA-CG-4304 
"7P GAIN WILD-TYPE"       "7P GAIN CNV" "7P GAIN WILD-TYPE"       "7P GAIN CNV" 
       TCGA-CG-4305        TCGA-CG-4306        TCGA-CG-4436        TCGA-CG-4437 
      "7P GAIN CNV" "7P GAIN WILD-TYPE"       "7P GAIN CNV" "7P GAIN WILD-TYPE" 
       TCGA-CG-4438        TCGA-CG-4440        TCGA-CG-4441        TCGA-CG-4443 
"7P GAIN WILD-TYPE" "7P GAIN WILD-TYPE" "7P GAIN WILD-TYPE" "7P GAIN WILD-TYPE" 
       TCGA-CG-4444        TCGA-CG-4449        TCGA-CG-4455        TCGA-CG-4460 
"7P GAIN WILD-TYPE" "7P GAIN WILD-TYPE" "7P GAIN WILD-TYPE"       "7P GAIN CNV" 
       TCGA-CG-4462        TCGA-CG-4465        TCGA-CG-4466        TCGA-CG-4469 
"7P GAIN WILD-TYPE" "7P GAIN WILD-TYPE" "7P GAIN WILD-TYPE"       "7P GAIN CNV" 
       TCGA-CG-4472        TCGA-CG-4474        TCGA-CG-4477        TCGA-CG-5716 
      "7P GAIN CNV"       "7P GAIN CNV" "7P GAIN WILD-TYPE" "7P GAIN WILD-TYPE" 
       TCGA-CG-5717        TCGA-CG-5718        TCGA-CG-5719        TCGA-CG-5720 
"7P GAIN WILD-TYPE"       "7P GAIN CNV" "7P GAIN WILD-TYPE" "7P GAIN WILD-TYPE" 
       TCGA-CG-5721        TCGA-CG-5722        TCGA-CG-5723        TCGA-CG-5724 
"7P GAIN WILD-TYPE" "7P GAIN WILD-TYPE" "7P GAIN WILD-TYPE"       "7P GAIN CNV" 
       TCGA-CG-5725        TCGA-CG-5726        TCGA-CG-5727        TCGA-CG-5728 
"7P GAIN WILD-TYPE"       "7P GAIN CNV"       "7P GAIN CNV" "7P GAIN WILD-TYPE" 
       TCGA-CG-5730        TCGA-CG-5732        TCGA-CG-5733        TCGA-CG-5734 
"7P GAIN WILD-TYPE" "7P GAIN WILD-TYPE"       "7P GAIN CNV" "7P GAIN WILD-TYPE" 
       TCGA-D7-5577        TCGA-D7-5578        TCGA-D7-5579        TCGA-D7-6518 
"7P GAIN WILD-TYPE" "7P GAIN WILD-TYPE" "7P GAIN WILD-TYPE"       "7P GAIN CNV" 
       TCGA-D7-6519        TCGA-D7-6520        TCGA-D7-6521        TCGA-D7-6522 
"7P GAIN WILD-TYPE" "7P GAIN WILD-TYPE"       "7P GAIN CNV" "7P GAIN WILD-TYPE" 
       TCGA-D7-6524        TCGA-D7-6525        TCGA-D7-6526        TCGA-D7-6527 
"7P GAIN WILD-TYPE" "7P GAIN WILD-TYPE"       "7P GAIN CNV" "7P GAIN WILD-TYPE" 
       TCGA-D7-6528        TCGA-D7-6815        TCGA-D7-6817        TCGA-D7-6818 
      "7P GAIN CNV" "7P GAIN WILD-TYPE" "7P GAIN WILD-TYPE"       "7P GAIN CNV" 
       TCGA-D7-6820        TCGA-D7-6822        TCGA-EQ-5647        TCGA-EQ-8122 
"7P GAIN WILD-TYPE"       "7P GAIN CNV" "7P GAIN WILD-TYPE" "7P GAIN WILD-TYPE" 
       TCGA-F1-6177        TCGA-F1-6874        TCGA-F1-6875        TCGA-FP-7735 
      "7P GAIN CNV"       "7P GAIN CNV"       "7P GAIN CNV"       "7P GAIN CNV" 
       TCGA-FP-7829        TCGA-FP-7916        TCGA-FP-7998        TCGA-FP-8099 
"7P GAIN WILD-TYPE" "7P GAIN WILD-TYPE" "7P GAIN WILD-TYPE"       "7P GAIN CNV" 
       TCGA-FP-8209        TCGA-FP-8210        TCGA-FP-8631        TCGA-HJ-7597 
"7P GAIN WILD-TYPE" "7P GAIN WILD-TYPE" "7P GAIN WILD-TYPE" "7P GAIN WILD-TYPE" 
       TCGA-IN-7806        TCGA-IN-7808        TCGA-IP-7968 
"7P GAIN WILD-TYPE"       "7P GAIN CNV" "7P GAIN WILD-TYPE" 
       TCGA-B7-5816        TCGA-B7-5818        TCGA-BR-6452        TCGA-BR-6455 
"7P GAIN WILD-TYPE"       "7P GAIN CNV" "7P GAIN WILD-TYPE" "7P GAIN WILD-TYPE" 
       TCGA-BR-6457        TCGA-BR-6458        TCGA-BR-6563        TCGA-BR-6564 
"7P GAIN WILD-TYPE" "7P GAIN WILD-TYPE" "7P GAIN WILD-TYPE" "7P GAIN WILD-TYPE" 
       TCGA-BR-6565        TCGA-BR-6566        TCGA-BR-6705        TCGA-BR-6706 
      "7P GAIN CNV"       "7P GAIN CNV" "7P GAIN WILD-TYPE" "7P GAIN WILD-TYPE" 
       TCGA-BR-6707        TCGA-BR-6709        TCGA-BR-6710        TCGA-BR-6801 
"7P GAIN WILD-TYPE" "7P GAIN WILD-TYPE" "7P GAIN WILD-TYPE"       "7P GAIN CNV" 
       TCGA-BR-6802        TCGA-BR-6803        TCGA-BR-6852        TCGA-BR-7196 
"7P GAIN WILD-TYPE" "7P GAIN WILD-TYPE" "7P GAIN WILD-TYPE" "7P GAIN WILD-TYPE" 
       TCGA-BR-7197        TCGA-BR-7703        TCGA-BR-7704        TCGA-BR-7707 
      "7P GAIN CNV" "7P GAIN WILD-TYPE"       "7P GAIN CNV" "7P GAIN WILD-TYPE" 
       TCGA-BR-7715        TCGA-BR-7716        TCGA-BR-7717        TCGA-BR-7722 
      "7P GAIN CNV" "7P GAIN WILD-TYPE"       "7P GAIN CNV" "7P GAIN WILD-TYPE" 
       TCGA-BR-7723        TCGA-BR-7851        TCGA-BR-7901        TCGA-BR-7957 
"7P GAIN WILD-TYPE" "7P GAIN WILD-TYPE"       "7P GAIN CNV" "7P GAIN WILD-TYPE" 
       TCGA-BR-7958        TCGA-BR-7959        TCGA-BR-8059        TCGA-BR-8060 
      "7P GAIN CNV" "7P GAIN WILD-TYPE" "7P GAIN WILD-TYPE" "7P GAIN WILD-TYPE" 
       TCGA-BR-8077        TCGA-BR-8078        TCGA-BR-8080        TCGA-BR-8081 
      "7P GAIN CNV" "7P GAIN WILD-TYPE" "7P GAIN WILD-TYPE" "7P GAIN WILD-TYPE" 
       TCGA-BR-8284        TCGA-BR-8285        TCGA-BR-8286        TCGA-BR-8289 
      "7P GAIN CNV"       "7P GAIN CNV"       "7P GAIN CNV" "7P GAIN WILD-TYPE" 
       TCGA-BR-8291        TCGA-BR-8295        TCGA-BR-8296        TCGA-BR-8297 
"7P GAIN WILD-TYPE"       "7P GAIN CNV" "7P GAIN WILD-TYPE" "7P GAIN WILD-TYPE" 
       TCGA-BR-8592        TCGA-BR-A4IU        TCGA-BR-A4IV        TCGA-BR-A4IY 
"7P GAIN WILD-TYPE" "7P GAIN WILD-TYPE" "7P GAIN WILD-TYPE"       "7P GAIN CNV" 
       TCGA-BR-A4IZ        TCGA-BR-A4J1        TCGA-BR-A4J2        TCGA-BR-A4J4 
"7P GAIN WILD-TYPE" "7P GAIN WILD-TYPE" "7P GAIN WILD-TYPE"       "7P GAIN CNV" 
       TCGA-BR-A4J5        TCGA-BR-A4J6        TCGA-BR-A4J8        TCGA-BR-A4J9 
"7P GAIN WILD-TYPE" "7P GAIN WILD-TYPE"       "7P GAIN CNV" "7P GAIN WILD-TYPE" 
       TCGA-BR-A4PF        TCGA-BR-A4QI        TCGA-BR-A4QL        TCGA-CD-5798 
"7P GAIN WILD-TYPE"       "7P GAIN CNV" "7P GAIN WILD-TYPE" "7P GAIN WILD-TYPE" 
       TCGA-CD-5799        TCGA-CD-5800        TCGA-CD-5801        TCGA-CD-5802 
"7P GAIN WILD-TYPE" "7P GAIN WILD-TYPE"       "7P GAIN CNV" "7P GAIN WILD-TYPE" 
       TCGA-CD-5803        TCGA-CG-4300        TCGA-CG-4301        TCGA-CG-4304 
"7P GAIN WILD-TYPE"       "7P GAIN CNV" "7P GAIN WILD-TYPE"       "7P GAIN CNV" 
       TCGA-CG-4305        TCGA-CG-4306        TCGA-CG-4436        TCGA-CG-4437 
      "7P GAIN CNV" "7P GAIN WILD-TYPE"       "7P GAIN CNV" "7P GAIN WILD-TYPE" 
       TCGA-CG-4438        TCGA-CG-4440        TCGA-CG-4441        TCGA-CG-4443 
"7P GAIN WILD-TYPE" "7P GAIN WILD-TYPE" "7P GAIN WILD-TYPE" "7P GAIN WILD-TYPE" 
       TCGA-CG-4444        TCGA-CG-4449        TCGA-CG-4455        TCGA-CG-4460 
"7P GAIN WILD-TYPE" "7P GAIN WILD-TYPE" "7P GAIN WILD-TYPE"       "7P GAIN CNV" 
       TCGA-CG-4462        TCGA-CG-4465        TCGA-CG-4466        TCGA-CG-4469 
"7P GAIN WILD-TYPE" "7P GAIN WILD-TYPE" "7P GAIN WILD-TYPE"       "7P GAIN CNV" 
       TCGA-CG-4472        TCGA-CG-4474        TCGA-CG-4477        TCGA-CG-5716 
      "7P GAIN CNV"       "7P GAIN CNV" "7P GAIN WILD-TYPE" "7P GAIN WILD-TYPE" 
       TCGA-CG-5717        TCGA-CG-5718        TCGA-CG-5719        TCGA-CG-5720 
"7P GAIN WILD-TYPE"       "7P GAIN CNV" "7P GAIN WILD-TYPE" "7P GAIN WILD-TYPE" 
       TCGA-CG-5721        TCGA-CG-5722        TCGA-CG-5723        TCGA-CG-5724 
"7P GAIN WILD-TYPE" "7P GAIN WILD-TYPE" "7P GAIN WILD-TYPE"       "7P GAIN CNV" 
       TCGA-CG-5725        TCGA-CG-5726        TCGA-CG-5727        TCGA-CG-5728 
"7P GAIN WILD-TYPE"       "7P GAIN CNV"       "7P GAIN CNV" "7P GAIN WILD-TYPE" 
       TCGA-CG-5730        TCGA-CG-5732        TCGA-CG-5733        TCGA-CG-5734 
"7P GAIN WILD-TYPE" "7P GAIN WILD-TYPE"       "7P GAIN CNV" "7P GAIN WILD-TYPE" 
       TCGA-D7-5577        TCGA-D7-5578        TCGA-D7-5579        TCGA-D7-6518 
"7P GAIN WILD-TYPE" "7P GAIN WILD-TYPE" "7P GAIN WILD-TYPE"       "7P GAIN CNV" 
       TCGA-D7-6519        TCGA-D7-6520        TCGA-D7-6521        TCGA-D7-6522 
"7P GAIN WILD-TYPE" "7P GAIN WILD-TYPE"       "7P GAIN CNV" "7P GAIN WILD-TYPE" 
       TCGA-D7-6524        TCGA-D7-6525        TCGA-D7-6526        TCGA-D7-6527 
"7P GAIN WILD-TYPE" "7P GAIN WILD-TYPE"       "7P GAIN CNV" "7P GAIN WILD-TYPE" 
       TCGA-D7-6528        TCGA-D7-6815        TCGA-D7-6817        TCGA-D7-6818 
      "7P GAIN CNV" "7P GAIN WILD-TYPE" "7P GAIN WILD-TYPE"       "7P GAIN CNV" 
       TCGA-D7-6820        TCGA-D7-6822        TCGA-EQ-5647        TCGA-EQ-8122 
"7P GAIN WILD-TYPE"       "7P GAIN CNV" "7P GAIN WILD-TYPE" "7P GAIN WILD-TYPE" 
       TCGA-F1-6177        TCGA-F1-6874        TCGA-F1-6875        TCGA-FP-7735 
      "7P GAIN CNV"       "7P GAIN CNV"       "7P GAIN CNV"       "7P GAIN CNV" 
       TCGA-FP-7829        TCGA-FP-7916        TCGA-FP-7998        TCGA-FP-8099 
"7P GAIN WILD-TYPE" "7P GAIN WILD-TYPE" "7P GAIN WILD-TYPE"       "7P GAIN CNV" 
       TCGA-FP-8209        TCGA-FP-8210        TCGA-FP-8631        TCGA-HJ-7597 
"7P GAIN WILD-TYPE" "7P GAIN WILD-TYPE" "7P GAIN WILD-TYPE" "7P GAIN WILD-TYPE" 
       TCGA-IN-7806        TCGA-IN-7808        TCGA-IP-7968 
"7P GAIN WILD-TYPE"       "7P GAIN CNV" "7P GAIN WILD-TYPE" 
[1] "hr=" "1.6"
D12V2, continuous
D12V3, binary
[1] "tbl2"
                   cls
clus                [,1] [,2]
  7P GAIN CNV         20   39
  7P GAIN WILD-TYPE   52   69
        clus
vv       7P GAIN CNV 7P GAIN WILD-TYPE
  FEMALE          20                52
  MALE            39                69
                   vv
clus                STOMACH  ADENOCARCINOMA  DIFFUSE TYPE
  7P GAIN CNV                                           0
  7P GAIN WILD-TYPE                                    10
                   vv
clus                STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  7P GAIN CNV                                                            8
  7P GAIN WILD-TYPE                                                      8
                   vv
clus                STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  7P GAIN CNV                                                                       3
  7P GAIN WILD-TYPE                                                                 5
                   vv
clus                STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE
  7P GAIN CNV                                                              0
  7P GAIN WILD-TYPE                                                        3
                   vv
clus                STOMACH ADENOCARCINOMA  SIGNET RING TYPE
  7P GAIN CNV                                              0
  7P GAIN WILD-TYPE                                        1
                   vv
clus                STOMACH ADENOCARCINOMA - DIFFUSE TYPE
  7P GAIN CNV                                           8
  7P GAIN WILD-TYPE                                     8
                   vv
clus                STOMACH ADENOCARCINOMA - NOT OTHERWISE SPECIFIED (NOS)
  7P GAIN CNV                                                           25
  7P GAIN WILD-TYPE                                                     48
                   vv
clus                STOMACH INTESTINAL ADENOCARCINOMA - MUCINOUS TYPE
  7P GAIN CNV                                                       0
  7P GAIN WILD-TYPE                                                 7
                   vv
clus                STOMACH INTESTINAL ADENOCARCINOMA - PAPILLARY TYPE
  7P GAIN CNV                                                        0
  7P GAIN WILD-TYPE                                                  3
                   vv
clus                STOMACH INTESTINAL ADENOCARCINOMA - TUBULAR TYPE
  7P GAIN CNV                                                      3
  7P GAIN WILD-TYPE                                                7
                   vv
clus                STOMACH INTESTINAL ADENOCARCINOMA - TYPE NOT OTHERWISE SPECIFIED (NOS)
  7P GAIN CNV                                                                           10
  7P GAIN WILD-TYPE                                                                     18
D12V4, multiclass
                   vv
clus                T1 T2 T3 T4
  7P GAIN CNV        3 16 18  7
  7P GAIN WILD-TYPE  3 36 38 11
D12V5, multiclass
    clus
vv   7P GAIN CNV 7P GAIN WILD-TYPE
  T1           3                 3
  T2          16                36
  T3          18                38
  T4           7                11
                   vv
clus                N0 N1 N2 N3
  7P GAIN CNV       19 14  6  6
  7P GAIN WILD-TYPE 25 35 17  9
D12V6, multiclass
    clus
vv   7P GAIN CNV 7P GAIN WILD-TYPE
  N0          19                25
  N1          14                35
  N2           6                17
  N3           6                 9
                   vv
clus                M0 M1 MX
  7P GAIN CNV       41  4  3
  7P GAIN WILD-TYPE 77 12  5
D12V7, multiclass
    clus
vv   7P GAIN CNV 7P GAIN WILD-TYPE
  M0          41                77
  M1           4                12
  MX           3                 5
                   vv
clus                 I II III IV
  7P GAIN CNV       12 11  11  9
  7P GAIN WILD-TYPE 12 26  28 17
D12V8, multiclass
     clus
vv    7P GAIN CNV 7P GAIN WILD-TYPE
  I            12                12
  II           11                26
  III          11                28
  IV            9                17
D12V9, binary
[1] "tbl2"
                   cls
clus                [,1] [,2]
  7P GAIN CNV          2   57
  7P GAIN WILD-TYPE    3  118
     clus
vv    7P GAIN CNV 7P GAIN WILD-TYPE
  NO            2                 3
  YES          57               118
                   vv
clus                R0 R1 R2 RX
  7P GAIN CNV       45  3  3  6
  7P GAIN WILD-TYPE 80  4  9 19
D12V10, multiclass
    clus
vv   7P GAIN CNV 7P GAIN WILD-TYPE
  R0          45                80
  R1           3                 4
  R2           3                 9
  RX           6                19
D12V11, continuous

Clustering(13) Variable = 7q gain
D13V1, survival
                   sevent
clus2                0  1
  7Q GAIN CNV       31  6
  7Q GAIN WILD-TYPE 93 13
      7Q GAIN CNV 7Q GAIN WILD-TYPE 
               37               106 
      7Q GAIN CNV 7Q GAIN WILD-TYPE 
                6                13 
$`7Q GAIN CNV`
TCGA-B7-5818 TCGA-BR-6565 TCGA-BR-6566 TCGA-BR-6801 TCGA-BR-7197 TCGA-BR-7704 
        0.10         0.62         0.62         1.12         1.48         1.25 
TCGA-BR-7715 TCGA-BR-7958 TCGA-BR-8284 TCGA-BR-8285 TCGA-BR-8295 TCGA-BR-A4IY 
        1.05         0.16         0.72         0.26         1.55         0.39 
TCGA-BR-A4J4 TCGA-BR-A4J8 TCGA-CD-5801 TCGA-CG-4300 TCGA-CG-4304 TCGA-CG-4305 
        0.53         0.23         0.49        20.02        27.02        15.95 
TCGA-CG-4436 TCGA-CG-4440 TCGA-CG-4469 TCGA-CG-4472 TCGA-CG-4474 TCGA-CG-5718 
       52.96         4.01         7.07        12.00         1.02         1.02 
TCGA-CG-5724 TCGA-CG-5726 TCGA-CG-5727 TCGA-CG-5733 TCGA-D7-6518 TCGA-D7-6521 
       12.03        28.96        31.04        21.07         9.80         8.19 
TCGA-D7-6526 TCGA-D7-6528 TCGA-F1-6177 TCGA-F1-6874 TCGA-F1-6875 TCGA-FP-7735 
        6.61         1.68         6.54         2.01        72.23         0.39 
TCGA-FP-8099 
        1.02 

$`7Q GAIN WILD-TYPE`
TCGA-B7-5816 TCGA-BR-6452 TCGA-BR-6455 TCGA-BR-6457 TCGA-BR-6458 TCGA-BR-6563 
        5.62         0.95         1.41         1.35         1.35         0.85 
TCGA-BR-6564 TCGA-BR-6705 TCGA-BR-6706 TCGA-BR-6707 TCGA-BR-6709 TCGA-BR-6710 
        0.82         1.71         2.17         0.99         1.22         0.66 
TCGA-BR-6802 TCGA-BR-6803 TCGA-BR-6852 TCGA-BR-7196 TCGA-BR-7703 TCGA-BR-7707 
        0.76         0.66         0.26         1.22         0.46         0.13 
TCGA-BR-7716 TCGA-BR-7717 TCGA-BR-7722 TCGA-BR-7723 TCGA-BR-7851 TCGA-BR-7901 
        0.82         0.69         0.16         4.54         0.99         0.95 
TCGA-BR-7957 TCGA-BR-7959 TCGA-BR-8059 TCGA-BR-8060 TCGA-BR-8077 TCGA-BR-8078 
        0.69         1.08         0.82         1.32         0.69         0.95 
TCGA-BR-8080 TCGA-BR-8081 TCGA-BR-8286 TCGA-BR-8289 TCGA-BR-8291 TCGA-BR-8296 
        0.49         0.46         0.43         0.26         1.18         1.48 
TCGA-BR-8297 TCGA-BR-8592 TCGA-BR-A4IU TCGA-BR-A4IV TCGA-BR-A4IZ TCGA-BR-A4J1 
        0.76         0.20         0.59         0.92         0.79         0.72 
TCGA-BR-A4J2 TCGA-BR-A4J5 TCGA-BR-A4J6 TCGA-BR-A4J9 TCGA-BR-A4PF TCGA-BR-A4QI 
        0.79         0.43         0.13         0.10         0.72         0.49 
TCGA-BR-A4QL TCGA-CD-5798 TCGA-CD-5799 TCGA-CD-5800 TCGA-CD-5802 TCGA-CD-5803 
        2.24         0.82         0.69         0.36         0.30         0.07 
TCGA-CG-4301 TCGA-CG-4306 TCGA-CG-4437 TCGA-CG-4438 TCGA-CG-4441 TCGA-CG-4443 
        3.02         1.02         8.05        54.05        14.01        29.98 
TCGA-CG-4444 TCGA-CG-4449 TCGA-CG-4455 TCGA-CG-4460 TCGA-CG-4462 TCGA-CG-4465 
       47.05        19.07        12.03        21.99         1.02         8.98 
TCGA-CG-4466 TCGA-CG-4477 TCGA-CG-5716 TCGA-CG-5717 TCGA-CG-5719 TCGA-CG-5720 
       18.94         1.02         1.02         6.94         1.02         0.99 
TCGA-CG-5721 TCGA-CG-5722 TCGA-CG-5723 TCGA-CG-5725 TCGA-CG-5728 TCGA-CG-5730 
        5.98         0.95        70.06        15.02        65.10         4.01 
TCGA-CG-5732 TCGA-CG-5734 TCGA-D7-5577 TCGA-D7-5578 TCGA-D7-5579 TCGA-D7-6519 
       55.04         7.99         8.65         3.58         4.54        15.65 
TCGA-D7-6520 TCGA-D7-6522 TCGA-D7-6524 TCGA-D7-6525 TCGA-D7-6527 TCGA-D7-6815 
        9.63         6.90         0.69         5.95         4.14         3.65 
TCGA-D7-6817 TCGA-D7-6818 TCGA-D7-6820 TCGA-D7-6822 TCGA-EQ-5647 TCGA-EQ-8122 
        4.70         4.04         2.93         4.27         0.62         7.79 
TCGA-FP-7829 TCGA-FP-7916 TCGA-FP-7998 TCGA-FP-8209 TCGA-FP-8210 TCGA-FP-8631 
        0.20         3.02         3.58        59.05         5.03         0.56 
TCGA-HJ-7597 TCGA-IN-7806 TCGA-IN-7808 TCGA-IP-7968 
       26.43         6.87         3.55         2.53 

      7Q GAIN CNV 7Q GAIN WILD-TYPE 
             0.10              0.07 
      7Q GAIN CNV 7Q GAIN WILD-TYPE 
            72.23             70.06 
      7Q GAIN CNV 7Q GAIN WILD-TYPE 
             1.55              1.20 
[1] "0.1 - 72.2 (1.6)" "0.1 - 70.1 (1.2)"
       TCGA-B7-5816        TCGA-B7-5818        TCGA-BR-6452        TCGA-BR-6455 
"7Q GAIN WILD-TYPE"       "7Q GAIN CNV" "7Q GAIN WILD-TYPE" "7Q GAIN WILD-TYPE" 
       TCGA-BR-6457        TCGA-BR-6458        TCGA-BR-6563        TCGA-BR-6564 
"7Q GAIN WILD-TYPE" "7Q GAIN WILD-TYPE" "7Q GAIN WILD-TYPE" "7Q GAIN WILD-TYPE" 
       TCGA-BR-6565        TCGA-BR-6566        TCGA-BR-6705        TCGA-BR-6706 
      "7Q GAIN CNV"       "7Q GAIN CNV" "7Q GAIN WILD-TYPE" "7Q GAIN WILD-TYPE" 
       TCGA-BR-6707        TCGA-BR-6709        TCGA-BR-6710        TCGA-BR-6801 
"7Q GAIN WILD-TYPE" "7Q GAIN WILD-TYPE" "7Q GAIN WILD-TYPE"       "7Q GAIN CNV" 
       TCGA-BR-6802        TCGA-BR-6803        TCGA-BR-6852        TCGA-BR-7196 
"7Q GAIN WILD-TYPE" "7Q GAIN WILD-TYPE" "7Q GAIN WILD-TYPE" "7Q GAIN WILD-TYPE" 
       TCGA-BR-7197        TCGA-BR-7703        TCGA-BR-7704        TCGA-BR-7707 
      "7Q GAIN CNV" "7Q GAIN WILD-TYPE"       "7Q GAIN CNV" "7Q GAIN WILD-TYPE" 
       TCGA-BR-7715        TCGA-BR-7716        TCGA-BR-7717        TCGA-BR-7722 
      "7Q GAIN CNV" "7Q GAIN WILD-TYPE" "7Q GAIN WILD-TYPE" "7Q GAIN WILD-TYPE" 
       TCGA-BR-7723        TCGA-BR-7851        TCGA-BR-7901        TCGA-BR-7957 
"7Q GAIN WILD-TYPE" "7Q GAIN WILD-TYPE" "7Q GAIN WILD-TYPE" "7Q GAIN WILD-TYPE" 
       TCGA-BR-7958        TCGA-BR-7959        TCGA-BR-8059        TCGA-BR-8060 
      "7Q GAIN CNV" "7Q GAIN WILD-TYPE" "7Q GAIN WILD-TYPE" "7Q GAIN WILD-TYPE" 
       TCGA-BR-8077        TCGA-BR-8078        TCGA-BR-8080        TCGA-BR-8081 
"7Q GAIN WILD-TYPE" "7Q GAIN WILD-TYPE" "7Q GAIN WILD-TYPE" "7Q GAIN WILD-TYPE" 
       TCGA-BR-8284        TCGA-BR-8285        TCGA-BR-8286        TCGA-BR-8289 
      "7Q GAIN CNV"       "7Q GAIN CNV" "7Q GAIN WILD-TYPE" "7Q GAIN WILD-TYPE" 
       TCGA-BR-8291        TCGA-BR-8295        TCGA-BR-8296        TCGA-BR-8297 
"7Q GAIN WILD-TYPE"       "7Q GAIN CNV" "7Q GAIN WILD-TYPE" "7Q GAIN WILD-TYPE" 
       TCGA-BR-8592        TCGA-BR-A4IU        TCGA-BR-A4IV        TCGA-BR-A4IY 
"7Q GAIN WILD-TYPE" "7Q GAIN WILD-TYPE" "7Q GAIN WILD-TYPE"       "7Q GAIN CNV" 
       TCGA-BR-A4IZ        TCGA-BR-A4J1        TCGA-BR-A4J2        TCGA-BR-A4J4 
"7Q GAIN WILD-TYPE" "7Q GAIN WILD-TYPE" "7Q GAIN WILD-TYPE"       "7Q GAIN CNV" 
       TCGA-BR-A4J5        TCGA-BR-A4J6        TCGA-BR-A4J8        TCGA-BR-A4J9 
"7Q GAIN WILD-TYPE" "7Q GAIN WILD-TYPE"       "7Q GAIN CNV" "7Q GAIN WILD-TYPE" 
       TCGA-BR-A4PF        TCGA-BR-A4QI        TCGA-BR-A4QL        TCGA-CD-5798 
"7Q GAIN WILD-TYPE" "7Q GAIN WILD-TYPE" "7Q GAIN WILD-TYPE" "7Q GAIN WILD-TYPE" 
       TCGA-CD-5799        TCGA-CD-5800        TCGA-CD-5801        TCGA-CD-5802 
"7Q GAIN WILD-TYPE" "7Q GAIN WILD-TYPE"       "7Q GAIN CNV" "7Q GAIN WILD-TYPE" 
       TCGA-CD-5803        TCGA-CG-4300        TCGA-CG-4301        TCGA-CG-4304 
"7Q GAIN WILD-TYPE"       "7Q GAIN CNV" "7Q GAIN WILD-TYPE"       "7Q GAIN CNV" 
       TCGA-CG-4305        TCGA-CG-4306        TCGA-CG-4436        TCGA-CG-4437 
      "7Q GAIN CNV" "7Q GAIN WILD-TYPE"       "7Q GAIN CNV" "7Q GAIN WILD-TYPE" 
       TCGA-CG-4438        TCGA-CG-4440        TCGA-CG-4441        TCGA-CG-4443 
"7Q GAIN WILD-TYPE"       "7Q GAIN CNV" "7Q GAIN WILD-TYPE" "7Q GAIN WILD-TYPE" 
       TCGA-CG-4444        TCGA-CG-4449        TCGA-CG-4455        TCGA-CG-4460 
"7Q GAIN WILD-TYPE" "7Q GAIN WILD-TYPE" "7Q GAIN WILD-TYPE" "7Q GAIN WILD-TYPE" 
       TCGA-CG-4462        TCGA-CG-4465        TCGA-CG-4466        TCGA-CG-4469 
"7Q GAIN WILD-TYPE" "7Q GAIN WILD-TYPE" "7Q GAIN WILD-TYPE"       "7Q GAIN CNV" 
       TCGA-CG-4472        TCGA-CG-4474        TCGA-CG-4477        TCGA-CG-5716 
      "7Q GAIN CNV"       "7Q GAIN CNV" "7Q GAIN WILD-TYPE" "7Q GAIN WILD-TYPE" 
       TCGA-CG-5717        TCGA-CG-5718        TCGA-CG-5719        TCGA-CG-5720 
"7Q GAIN WILD-TYPE"       "7Q GAIN CNV" "7Q GAIN WILD-TYPE" "7Q GAIN WILD-TYPE" 
       TCGA-CG-5721        TCGA-CG-5722        TCGA-CG-5723        TCGA-CG-5724 
"7Q GAIN WILD-TYPE" "7Q GAIN WILD-TYPE" "7Q GAIN WILD-TYPE"       "7Q GAIN CNV" 
       TCGA-CG-5725        TCGA-CG-5726        TCGA-CG-5727        TCGA-CG-5728 
"7Q GAIN WILD-TYPE"       "7Q GAIN CNV"       "7Q GAIN CNV" "7Q GAIN WILD-TYPE" 
       TCGA-CG-5730        TCGA-CG-5732        TCGA-CG-5733        TCGA-CG-5734 
"7Q GAIN WILD-TYPE" "7Q GAIN WILD-TYPE"       "7Q GAIN CNV" "7Q GAIN WILD-TYPE" 
       TCGA-D7-5577        TCGA-D7-5578        TCGA-D7-5579        TCGA-D7-6518 
"7Q GAIN WILD-TYPE" "7Q GAIN WILD-TYPE" "7Q GAIN WILD-TYPE"       "7Q GAIN CNV" 
       TCGA-D7-6519        TCGA-D7-6520        TCGA-D7-6521        TCGA-D7-6522 
"7Q GAIN WILD-TYPE" "7Q GAIN WILD-TYPE"       "7Q GAIN CNV" "7Q GAIN WILD-TYPE" 
       TCGA-D7-6524        TCGA-D7-6525        TCGA-D7-6526        TCGA-D7-6527 
"7Q GAIN WILD-TYPE" "7Q GAIN WILD-TYPE"       "7Q GAIN CNV" "7Q GAIN WILD-TYPE" 
       TCGA-D7-6528        TCGA-D7-6815        TCGA-D7-6817        TCGA-D7-6818 
      "7Q GAIN CNV" "7Q GAIN WILD-TYPE" "7Q GAIN WILD-TYPE" "7Q GAIN WILD-TYPE" 
       TCGA-D7-6820        TCGA-D7-6822        TCGA-EQ-5647        TCGA-EQ-8122 
"7Q GAIN WILD-TYPE" "7Q GAIN WILD-TYPE" "7Q GAIN WILD-TYPE" "7Q GAIN WILD-TYPE" 
       TCGA-F1-6177        TCGA-F1-6874        TCGA-F1-6875        TCGA-FP-7735 
      "7Q GAIN CNV"       "7Q GAIN CNV"       "7Q GAIN CNV"       "7Q GAIN CNV" 
       TCGA-FP-7829        TCGA-FP-7916        TCGA-FP-7998        TCGA-FP-8099 
"7Q GAIN WILD-TYPE" "7Q GAIN WILD-TYPE" "7Q GAIN WILD-TYPE"       "7Q GAIN CNV" 
       TCGA-FP-8209        TCGA-FP-8210        TCGA-FP-8631        TCGA-HJ-7597 
"7Q GAIN WILD-TYPE" "7Q GAIN WILD-TYPE" "7Q GAIN WILD-TYPE" "7Q GAIN WILD-TYPE" 
       TCGA-IN-7806        TCGA-IN-7808        TCGA-IP-7968 
"7Q GAIN WILD-TYPE" "7Q GAIN WILD-TYPE" "7Q GAIN WILD-TYPE" 
       TCGA-B7-5816        TCGA-B7-5818        TCGA-BR-6452        TCGA-BR-6455 
"7Q GAIN WILD-TYPE"       "7Q GAIN CNV" "7Q GAIN WILD-TYPE" "7Q GAIN WILD-TYPE" 
       TCGA-BR-6457        TCGA-BR-6458        TCGA-BR-6563        TCGA-BR-6564 
"7Q GAIN WILD-TYPE" "7Q GAIN WILD-TYPE" "7Q GAIN WILD-TYPE" "7Q GAIN WILD-TYPE" 
       TCGA-BR-6565        TCGA-BR-6566        TCGA-BR-6705        TCGA-BR-6706 
      "7Q GAIN CNV"       "7Q GAIN CNV" "7Q GAIN WILD-TYPE" "7Q GAIN WILD-TYPE" 
       TCGA-BR-6707        TCGA-BR-6709        TCGA-BR-6710        TCGA-BR-6801 
"7Q GAIN WILD-TYPE" "7Q GAIN WILD-TYPE" "7Q GAIN WILD-TYPE"       "7Q GAIN CNV" 
       TCGA-BR-6802        TCGA-BR-6803        TCGA-BR-6852        TCGA-BR-7196 
"7Q GAIN WILD-TYPE" "7Q GAIN WILD-TYPE" "7Q GAIN WILD-TYPE" "7Q GAIN WILD-TYPE" 
       TCGA-BR-7197        TCGA-BR-7703        TCGA-BR-7704        TCGA-BR-7707 
      "7Q GAIN CNV" "7Q GAIN WILD-TYPE"       "7Q GAIN CNV" "7Q GAIN WILD-TYPE" 
       TCGA-BR-7715        TCGA-BR-7716        TCGA-BR-7717        TCGA-BR-7722 
      "7Q GAIN CNV" "7Q GAIN WILD-TYPE" "7Q GAIN WILD-TYPE" "7Q GAIN WILD-TYPE" 
       TCGA-BR-7723        TCGA-BR-7851        TCGA-BR-7901        TCGA-BR-7957 
"7Q GAIN WILD-TYPE" "7Q GAIN WILD-TYPE" "7Q GAIN WILD-TYPE" "7Q GAIN WILD-TYPE" 
       TCGA-BR-7958        TCGA-BR-7959        TCGA-BR-8059        TCGA-BR-8060 
      "7Q GAIN CNV" "7Q GAIN WILD-TYPE" "7Q GAIN WILD-TYPE" "7Q GAIN WILD-TYPE" 
       TCGA-BR-8077        TCGA-BR-8078        TCGA-BR-8080        TCGA-BR-8081 
"7Q GAIN WILD-TYPE" "7Q GAIN WILD-TYPE" "7Q GAIN WILD-TYPE" "7Q GAIN WILD-TYPE" 
       TCGA-BR-8284        TCGA-BR-8285        TCGA-BR-8286        TCGA-BR-8289 
      "7Q GAIN CNV"       "7Q GAIN CNV" "7Q GAIN WILD-TYPE" "7Q GAIN WILD-TYPE" 
       TCGA-BR-8291        TCGA-BR-8295        TCGA-BR-8296        TCGA-BR-8297 
"7Q GAIN WILD-TYPE"       "7Q GAIN CNV" "7Q GAIN WILD-TYPE" "7Q GAIN WILD-TYPE" 
       TCGA-BR-8592        TCGA-BR-A4IU        TCGA-BR-A4IV        TCGA-BR-A4IY 
"7Q GAIN WILD-TYPE" "7Q GAIN WILD-TYPE" "7Q GAIN WILD-TYPE"       "7Q GAIN CNV" 
       TCGA-BR-A4IZ        TCGA-BR-A4J1        TCGA-BR-A4J2        TCGA-BR-A4J4 
"7Q GAIN WILD-TYPE" "7Q GAIN WILD-TYPE" "7Q GAIN WILD-TYPE"       "7Q GAIN CNV" 
       TCGA-BR-A4J5        TCGA-BR-A4J6        TCGA-BR-A4J8        TCGA-BR-A4J9 
"7Q GAIN WILD-TYPE" "7Q GAIN WILD-TYPE"       "7Q GAIN CNV" "7Q GAIN WILD-TYPE" 
       TCGA-BR-A4PF        TCGA-BR-A4QI        TCGA-BR-A4QL        TCGA-CD-5798 
"7Q GAIN WILD-TYPE" "7Q GAIN WILD-TYPE" "7Q GAIN WILD-TYPE" "7Q GAIN WILD-TYPE" 
       TCGA-CD-5799        TCGA-CD-5800        TCGA-CD-5801        TCGA-CD-5802 
"7Q GAIN WILD-TYPE" "7Q GAIN WILD-TYPE"       "7Q GAIN CNV" "7Q GAIN WILD-TYPE" 
       TCGA-CD-5803        TCGA-CG-4300        TCGA-CG-4301        TCGA-CG-4304 
"7Q GAIN WILD-TYPE"       "7Q GAIN CNV" "7Q GAIN WILD-TYPE"       "7Q GAIN CNV" 
       TCGA-CG-4305        TCGA-CG-4306        TCGA-CG-4436        TCGA-CG-4437 
      "7Q GAIN CNV" "7Q GAIN WILD-TYPE"       "7Q GAIN CNV" "7Q GAIN WILD-TYPE" 
       TCGA-CG-4438        TCGA-CG-4440        TCGA-CG-4441        TCGA-CG-4443 
"7Q GAIN WILD-TYPE"       "7Q GAIN CNV" "7Q GAIN WILD-TYPE" "7Q GAIN WILD-TYPE" 
       TCGA-CG-4444        TCGA-CG-4449        TCGA-CG-4455        TCGA-CG-4460 
"7Q GAIN WILD-TYPE" "7Q GAIN WILD-TYPE" "7Q GAIN WILD-TYPE" "7Q GAIN WILD-TYPE" 
       TCGA-CG-4462        TCGA-CG-4465        TCGA-CG-4466        TCGA-CG-4469 
"7Q GAIN WILD-TYPE" "7Q GAIN WILD-TYPE" "7Q GAIN WILD-TYPE"       "7Q GAIN CNV" 
       TCGA-CG-4472        TCGA-CG-4474        TCGA-CG-4477        TCGA-CG-5716 
      "7Q GAIN CNV"       "7Q GAIN CNV" "7Q GAIN WILD-TYPE" "7Q GAIN WILD-TYPE" 
       TCGA-CG-5717        TCGA-CG-5718        TCGA-CG-5719        TCGA-CG-5720 
"7Q GAIN WILD-TYPE"       "7Q GAIN CNV" "7Q GAIN WILD-TYPE" "7Q GAIN WILD-TYPE" 
       TCGA-CG-5721        TCGA-CG-5722        TCGA-CG-5723        TCGA-CG-5724 
"7Q GAIN WILD-TYPE" "7Q GAIN WILD-TYPE" "7Q GAIN WILD-TYPE"       "7Q GAIN CNV" 
       TCGA-CG-5725        TCGA-CG-5726        TCGA-CG-5727        TCGA-CG-5728 
"7Q GAIN WILD-TYPE"       "7Q GAIN CNV"       "7Q GAIN CNV" "7Q GAIN WILD-TYPE" 
       TCGA-CG-5730        TCGA-CG-5732        TCGA-CG-5733        TCGA-CG-5734 
"7Q GAIN WILD-TYPE" "7Q GAIN WILD-TYPE"       "7Q GAIN CNV" "7Q GAIN WILD-TYPE" 
       TCGA-D7-5577        TCGA-D7-5578        TCGA-D7-5579        TCGA-D7-6518 
"7Q GAIN WILD-TYPE" "7Q GAIN WILD-TYPE" "7Q GAIN WILD-TYPE"       "7Q GAIN CNV" 
       TCGA-D7-6519        TCGA-D7-6520        TCGA-D7-6521        TCGA-D7-6522 
"7Q GAIN WILD-TYPE" "7Q GAIN WILD-TYPE"       "7Q GAIN CNV" "7Q GAIN WILD-TYPE" 
       TCGA-D7-6524        TCGA-D7-6525        TCGA-D7-6526        TCGA-D7-6527 
"7Q GAIN WILD-TYPE" "7Q GAIN WILD-TYPE"       "7Q GAIN CNV" "7Q GAIN WILD-TYPE" 
       TCGA-D7-6528        TCGA-D7-6815        TCGA-D7-6817        TCGA-D7-6818 
      "7Q GAIN CNV" "7Q GAIN WILD-TYPE" "7Q GAIN WILD-TYPE" "7Q GAIN WILD-TYPE" 
       TCGA-D7-6820        TCGA-D7-6822        TCGA-EQ-5647        TCGA-EQ-8122 
"7Q GAIN WILD-TYPE" "7Q GAIN WILD-TYPE" "7Q GAIN WILD-TYPE" "7Q GAIN WILD-TYPE" 
       TCGA-F1-6177        TCGA-F1-6874        TCGA-F1-6875        TCGA-FP-7735 
      "7Q GAIN CNV"       "7Q GAIN CNV"       "7Q GAIN CNV"       "7Q GAIN CNV" 
       TCGA-FP-7829        TCGA-FP-7916        TCGA-FP-7998        TCGA-FP-8099 
"7Q GAIN WILD-TYPE" "7Q GAIN WILD-TYPE" "7Q GAIN WILD-TYPE"       "7Q GAIN CNV" 
       TCGA-FP-8209        TCGA-FP-8210        TCGA-FP-8631        TCGA-HJ-7597 
"7Q GAIN WILD-TYPE" "7Q GAIN WILD-TYPE" "7Q GAIN WILD-TYPE" "7Q GAIN WILD-TYPE" 
       TCGA-IN-7806        TCGA-IN-7808        TCGA-IP-7968 
"7Q GAIN WILD-TYPE" "7Q GAIN WILD-TYPE" "7Q GAIN WILD-TYPE" 
       TCGA-B7-5816        TCGA-B7-5818        TCGA-BR-6452        TCGA-BR-6455 
"7Q GAIN WILD-TYPE"       "7Q GAIN CNV" "7Q GAIN WILD-TYPE" "7Q GAIN WILD-TYPE" 
       TCGA-BR-6457        TCGA-BR-6458        TCGA-BR-6563        TCGA-BR-6564 
"7Q GAIN WILD-TYPE" "7Q GAIN WILD-TYPE" "7Q GAIN WILD-TYPE" "7Q GAIN WILD-TYPE" 
       TCGA-BR-6565        TCGA-BR-6566        TCGA-BR-6705        TCGA-BR-6706 
      "7Q GAIN CNV"       "7Q GAIN CNV" "7Q GAIN WILD-TYPE" "7Q GAIN WILD-TYPE" 
       TCGA-BR-6707        TCGA-BR-6709        TCGA-BR-6710        TCGA-BR-6801 
"7Q GAIN WILD-TYPE" "7Q GAIN WILD-TYPE" "7Q GAIN WILD-TYPE"       "7Q GAIN CNV" 
       TCGA-BR-6802        TCGA-BR-6803        TCGA-BR-6852        TCGA-BR-7196 
"7Q GAIN WILD-TYPE" "7Q GAIN WILD-TYPE" "7Q GAIN WILD-TYPE" "7Q GAIN WILD-TYPE" 
       TCGA-BR-7197        TCGA-BR-7703        TCGA-BR-7704        TCGA-BR-7707 
      "7Q GAIN CNV" "7Q GAIN WILD-TYPE"       "7Q GAIN CNV" "7Q GAIN WILD-TYPE" 
       TCGA-BR-7715        TCGA-BR-7716        TCGA-BR-7717        TCGA-BR-7722 
      "7Q GAIN CNV" "7Q GAIN WILD-TYPE" "7Q GAIN WILD-TYPE" "7Q GAIN WILD-TYPE" 
       TCGA-BR-7723        TCGA-BR-7851        TCGA-BR-7901        TCGA-BR-7957 
"7Q GAIN WILD-TYPE" "7Q GAIN WILD-TYPE" "7Q GAIN WILD-TYPE" "7Q GAIN WILD-TYPE" 
       TCGA-BR-7958        TCGA-BR-7959        TCGA-BR-8059        TCGA-BR-8060 
      "7Q GAIN CNV" "7Q GAIN WILD-TYPE" "7Q GAIN WILD-TYPE" "7Q GAIN WILD-TYPE" 
       TCGA-BR-8077        TCGA-BR-8078        TCGA-BR-8080        TCGA-BR-8081 
"7Q GAIN WILD-TYPE" "7Q GAIN WILD-TYPE" "7Q GAIN WILD-TYPE" "7Q GAIN WILD-TYPE" 
       TCGA-BR-8284        TCGA-BR-8285        TCGA-BR-8286        TCGA-BR-8289 
      "7Q GAIN CNV"       "7Q GAIN CNV" "7Q GAIN WILD-TYPE" "7Q GAIN WILD-TYPE" 
       TCGA-BR-8291        TCGA-BR-8295        TCGA-BR-8296        TCGA-BR-8297 
"7Q GAIN WILD-TYPE"       "7Q GAIN CNV" "7Q GAIN WILD-TYPE" "7Q GAIN WILD-TYPE" 
       TCGA-BR-8592        TCGA-BR-A4IU        TCGA-BR-A4IV        TCGA-BR-A4IY 
"7Q GAIN WILD-TYPE" "7Q GAIN WILD-TYPE" "7Q GAIN WILD-TYPE"       "7Q GAIN CNV" 
       TCGA-BR-A4IZ        TCGA-BR-A4J1        TCGA-BR-A4J2        TCGA-BR-A4J4 
"7Q GAIN WILD-TYPE" "7Q GAIN WILD-TYPE" "7Q GAIN WILD-TYPE"       "7Q GAIN CNV" 
       TCGA-BR-A4J5        TCGA-BR-A4J6        TCGA-BR-A4J8        TCGA-BR-A4J9 
"7Q GAIN WILD-TYPE" "7Q GAIN WILD-TYPE"       "7Q GAIN CNV" "7Q GAIN WILD-TYPE" 
       TCGA-BR-A4PF        TCGA-BR-A4QI        TCGA-BR-A4QL        TCGA-CD-5798 
"7Q GAIN WILD-TYPE" "7Q GAIN WILD-TYPE" "7Q GAIN WILD-TYPE" "7Q GAIN WILD-TYPE" 
       TCGA-CD-5799        TCGA-CD-5800        TCGA-CD-5801        TCGA-CD-5802 
"7Q GAIN WILD-TYPE" "7Q GAIN WILD-TYPE"       "7Q GAIN CNV" "7Q GAIN WILD-TYPE" 
       TCGA-CD-5803        TCGA-CG-4300        TCGA-CG-4301        TCGA-CG-4304 
"7Q GAIN WILD-TYPE"       "7Q GAIN CNV" "7Q GAIN WILD-TYPE"       "7Q GAIN CNV" 
       TCGA-CG-4305        TCGA-CG-4306        TCGA-CG-4436        TCGA-CG-4437 
      "7Q GAIN CNV" "7Q GAIN WILD-TYPE"       "7Q GAIN CNV" "7Q GAIN WILD-TYPE" 
       TCGA-CG-4438        TCGA-CG-4440        TCGA-CG-4441        TCGA-CG-4443 
"7Q GAIN WILD-TYPE"       "7Q GAIN CNV" "7Q GAIN WILD-TYPE" "7Q GAIN WILD-TYPE" 
       TCGA-CG-4444        TCGA-CG-4449        TCGA-CG-4455        TCGA-CG-4460 
"7Q GAIN WILD-TYPE" "7Q GAIN WILD-TYPE" "7Q GAIN WILD-TYPE" "7Q GAIN WILD-TYPE" 
       TCGA-CG-4462        TCGA-CG-4465        TCGA-CG-4466        TCGA-CG-4469 
"7Q GAIN WILD-TYPE" "7Q GAIN WILD-TYPE" "7Q GAIN WILD-TYPE"       "7Q GAIN CNV" 
       TCGA-CG-4472        TCGA-CG-4474        TCGA-CG-4477        TCGA-CG-5716 
      "7Q GAIN CNV"       "7Q GAIN CNV" "7Q GAIN WILD-TYPE" "7Q GAIN WILD-TYPE" 
       TCGA-CG-5717        TCGA-CG-5718        TCGA-CG-5719        TCGA-CG-5720 
"7Q GAIN WILD-TYPE"       "7Q GAIN CNV" "7Q GAIN WILD-TYPE" "7Q GAIN WILD-TYPE" 
       TCGA-CG-5721        TCGA-CG-5722        TCGA-CG-5723        TCGA-CG-5724 
"7Q GAIN WILD-TYPE" "7Q GAIN WILD-TYPE" "7Q GAIN WILD-TYPE"       "7Q GAIN CNV" 
       TCGA-CG-5725        TCGA-CG-5726        TCGA-CG-5727        TCGA-CG-5728 
"7Q GAIN WILD-TYPE"       "7Q GAIN CNV"       "7Q GAIN CNV" "7Q GAIN WILD-TYPE" 
       TCGA-CG-5730        TCGA-CG-5732        TCGA-CG-5733        TCGA-CG-5734 
"7Q GAIN WILD-TYPE" "7Q GAIN WILD-TYPE"       "7Q GAIN CNV" "7Q GAIN WILD-TYPE" 
       TCGA-D7-5577        TCGA-D7-5578        TCGA-D7-5579        TCGA-D7-6518 
"7Q GAIN WILD-TYPE" "7Q GAIN WILD-TYPE" "7Q GAIN WILD-TYPE"       "7Q GAIN CNV" 
       TCGA-D7-6519        TCGA-D7-6520        TCGA-D7-6521        TCGA-D7-6522 
"7Q GAIN WILD-TYPE" "7Q GAIN WILD-TYPE"       "7Q GAIN CNV" "7Q GAIN WILD-TYPE" 
       TCGA-D7-6524        TCGA-D7-6525        TCGA-D7-6526        TCGA-D7-6527 
"7Q GAIN WILD-TYPE" "7Q GAIN WILD-TYPE"       "7Q GAIN CNV" "7Q GAIN WILD-TYPE" 
       TCGA-D7-6528        TCGA-D7-6815        TCGA-D7-6817        TCGA-D7-6818 
      "7Q GAIN CNV" "7Q GAIN WILD-TYPE" "7Q GAIN WILD-TYPE" "7Q GAIN WILD-TYPE" 
       TCGA-D7-6820        TCGA-D7-6822        TCGA-EQ-5647        TCGA-EQ-8122 
"7Q GAIN WILD-TYPE" "7Q GAIN WILD-TYPE" "7Q GAIN WILD-TYPE" "7Q GAIN WILD-TYPE" 
       TCGA-F1-6177        TCGA-F1-6874        TCGA-F1-6875        TCGA-FP-7735 
      "7Q GAIN CNV"       "7Q GAIN CNV"       "7Q GAIN CNV"       "7Q GAIN CNV" 
       TCGA-FP-7829        TCGA-FP-7916        TCGA-FP-7998        TCGA-FP-8099 
"7Q GAIN WILD-TYPE" "7Q GAIN WILD-TYPE" "7Q GAIN WILD-TYPE"       "7Q GAIN CNV" 
       TCGA-FP-8209        TCGA-FP-8210        TCGA-FP-8631        TCGA-HJ-7597 
"7Q GAIN WILD-TYPE" "7Q GAIN WILD-TYPE" "7Q GAIN WILD-TYPE" "7Q GAIN WILD-TYPE" 
       TCGA-IN-7806        TCGA-IN-7808        TCGA-IP-7968 
"7Q GAIN WILD-TYPE" "7Q GAIN WILD-TYPE" "7Q GAIN WILD-TYPE" 
[1] "hr=" "1.4"
D13V2, continuous
D13V3, binary
[1] "tbl2"
                   cls
clus                [,1] [,2]
  7Q GAIN CNV         18   33
  7Q GAIN WILD-TYPE   54   75
        clus
vv       7Q GAIN CNV 7Q GAIN WILD-TYPE
  FEMALE          18                54
  MALE            33                75
                   vv
clus                STOMACH  ADENOCARCINOMA  DIFFUSE TYPE
  7Q GAIN CNV                                           0
  7Q GAIN WILD-TYPE                                    10
                   vv
clus                STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  7Q GAIN CNV                                                            6
  7Q GAIN WILD-TYPE                                                     10
                   vv
clus                STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  7Q GAIN CNV                                                                       2
  7Q GAIN WILD-TYPE                                                                 6
                   vv
clus                STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE
  7Q GAIN CNV                                                              0
  7Q GAIN WILD-TYPE                                                        3
                   vv
clus                STOMACH ADENOCARCINOMA  SIGNET RING TYPE
  7Q GAIN CNV                                              0
  7Q GAIN WILD-TYPE                                        1
                   vv
clus                STOMACH ADENOCARCINOMA - DIFFUSE TYPE
  7Q GAIN CNV                                           6
  7Q GAIN WILD-TYPE                                    10
                   vv
clus                STOMACH ADENOCARCINOMA - NOT OTHERWISE SPECIFIED (NOS)
  7Q GAIN CNV                                                           23
  7Q GAIN WILD-TYPE                                                     50
                   vv
clus                STOMACH INTESTINAL ADENOCARCINOMA - MUCINOUS TYPE
  7Q GAIN CNV                                                       0
  7Q GAIN WILD-TYPE                                                 7
                   vv
clus                STOMACH INTESTINAL ADENOCARCINOMA - PAPILLARY TYPE
  7Q GAIN CNV                                                        0
  7Q GAIN WILD-TYPE                                                  3
                   vv
clus                STOMACH INTESTINAL ADENOCARCINOMA - TUBULAR TYPE
  7Q GAIN CNV                                                      2
  7Q GAIN WILD-TYPE                                                8
                   vv
clus                STOMACH INTESTINAL ADENOCARCINOMA - TYPE NOT OTHERWISE SPECIFIED (NOS)
  7Q GAIN CNV                                                                           10
  7Q GAIN WILD-TYPE                                                                     18
D13V4, multiclass
                   vv
clus                T1 T2 T3 T4
  7Q GAIN CNV        3 14 17  5
  7Q GAIN WILD-TYPE  3 38 39 13
D13V5, multiclass
    clus
vv   7Q GAIN CNV 7Q GAIN WILD-TYPE
  T1           3                 3
  T2          14                38
  T3          17                39
  T4           5                13
                   vv
clus                N0 N1 N2 N3
  7Q GAIN CNV       17 12  6  5
  7Q GAIN WILD-TYPE 27 37 17 10
D13V6, multiclass
    clus
vv   7Q GAIN CNV 7Q GAIN WILD-TYPE
  N0          17                27
  N1          12                37
  N2           6                17
  N3           5                10
                   vv
clus                M0 M1 MX
  7Q GAIN CNV       36  3  4
  7Q GAIN WILD-TYPE 82 13  4
D13V7, multiclass
    clus
vv   7Q GAIN CNV 7Q GAIN WILD-TYPE
  M0          36                82
  M1           3                13
  MX           4                 4
                   vv
clus                 I II III IV
  7Q GAIN CNV       11 10   9  7
  7Q GAIN WILD-TYPE 13 27  30 19
D13V8, multiclass
     clus
vv    7Q GAIN CNV 7Q GAIN WILD-TYPE
  I            11                13
  II           10                27
  III           9                30
  IV            7                19
D13V9, binary
[1] "tbl2"
                   cls
clus                [,1] [,2]
  7Q GAIN CNV          1   50
  7Q GAIN WILD-TYPE    4  125
     clus
vv    7Q GAIN CNV 7Q GAIN WILD-TYPE
  NO            1                 4
  YES          50               125
                   vv
clus                R0 R1 R2 RX
  7Q GAIN CNV       37  3  3  7
  7Q GAIN WILD-TYPE 88  4  9 18
D13V10, multiclass
    clus
vv   7Q GAIN CNV 7Q GAIN WILD-TYPE
  R0          37                88
  R1           3                 4
  R2           3                 9
  RX           7                18
D13V11, continuous

Clustering(14) Variable = 8p gain
D14V1, survival
                   sevent
clus2                0  1
  8P GAIN CNV       31  7
  8P GAIN WILD-TYPE 93 12
      8P GAIN CNV 8P GAIN WILD-TYPE 
               38               105 
      8P GAIN CNV 8P GAIN WILD-TYPE 
                7                12 
$`8P GAIN CNV`
TCGA-B7-5816 TCGA-BR-6452 TCGA-BR-6455 TCGA-BR-6707 TCGA-BR-6852 TCGA-BR-7704 
        5.62         0.95         1.41         0.99         0.26         1.25 
TCGA-BR-7707 TCGA-BR-7715 TCGA-BR-8078 TCGA-BR-8080 TCGA-BR-8284 TCGA-BR-8297 
        0.13         1.05         0.95         0.49         0.72         0.76 
TCGA-BR-A4QL TCGA-CG-4305 TCGA-CG-4441 TCGA-CG-4444 TCGA-CG-4455 TCGA-CG-4460 
        2.24        15.95        14.01        47.05        12.03        21.99 
TCGA-CG-4466 TCGA-CG-4469 TCGA-CG-4472 TCGA-CG-5718 TCGA-CG-5725 TCGA-CG-5726 
       18.94         7.07        12.00         1.02        15.02        28.96 
TCGA-CG-5727 TCGA-CG-5728 TCGA-CG-5733 TCGA-D7-5578 TCGA-D7-5579 TCGA-D7-6520 
       31.04        65.10        21.07         3.58         4.54         9.63 
TCGA-D7-6524 TCGA-D7-6526 TCGA-D7-6817 TCGA-D7-6818 TCGA-D7-6822 TCGA-EQ-5647 
        0.69         6.61         4.70         4.04         4.27         0.62 
TCGA-FP-7829 TCGA-IN-7808 
        0.20         3.55 

$`8P GAIN WILD-TYPE`
TCGA-B7-5818 TCGA-BR-6457 TCGA-BR-6458 TCGA-BR-6563 TCGA-BR-6564 TCGA-BR-6565 
        0.10         1.35         1.35         0.85         0.82         0.62 
TCGA-BR-6566 TCGA-BR-6705 TCGA-BR-6706 TCGA-BR-6709 TCGA-BR-6710 TCGA-BR-6801 
        0.62         1.71         2.17         1.22         0.66         1.12 
TCGA-BR-6802 TCGA-BR-6803 TCGA-BR-7196 TCGA-BR-7197 TCGA-BR-7703 TCGA-BR-7716 
        0.76         0.66         1.22         1.48         0.46         0.82 
TCGA-BR-7717 TCGA-BR-7722 TCGA-BR-7723 TCGA-BR-7851 TCGA-BR-7901 TCGA-BR-7957 
        0.69         0.16         4.54         0.99         0.95         0.69 
TCGA-BR-7958 TCGA-BR-7959 TCGA-BR-8059 TCGA-BR-8060 TCGA-BR-8077 TCGA-BR-8081 
        0.16         1.08         0.82         1.32         0.69         0.46 
TCGA-BR-8285 TCGA-BR-8286 TCGA-BR-8289 TCGA-BR-8291 TCGA-BR-8295 TCGA-BR-8296 
        0.26         0.43         0.26         1.18         1.55         1.48 
TCGA-BR-8592 TCGA-BR-A4IU TCGA-BR-A4IV TCGA-BR-A4IY TCGA-BR-A4IZ TCGA-BR-A4J1 
        0.20         0.59         0.92         0.39         0.79         0.72 
TCGA-BR-A4J2 TCGA-BR-A4J4 TCGA-BR-A4J5 TCGA-BR-A4J6 TCGA-BR-A4J8 TCGA-BR-A4J9 
        0.79         0.53         0.43         0.13         0.23         0.10 
TCGA-BR-A4PF TCGA-BR-A4QI TCGA-CD-5798 TCGA-CD-5799 TCGA-CD-5800 TCGA-CD-5801 
        0.72         0.49         0.82         0.69         0.36         0.49 
TCGA-CD-5802 TCGA-CD-5803 TCGA-CG-4300 TCGA-CG-4301 TCGA-CG-4304 TCGA-CG-4306 
        0.30         0.07        20.02         3.02        27.02         1.02 
TCGA-CG-4436 TCGA-CG-4437 TCGA-CG-4438 TCGA-CG-4440 TCGA-CG-4443 TCGA-CG-4449 
       52.96         8.05        54.05         4.01        29.98        19.07 
TCGA-CG-4462 TCGA-CG-4465 TCGA-CG-4474 TCGA-CG-4477 TCGA-CG-5716 TCGA-CG-5717 
        1.02         8.98         1.02         1.02         1.02         6.94 
TCGA-CG-5719 TCGA-CG-5720 TCGA-CG-5721 TCGA-CG-5722 TCGA-CG-5723 TCGA-CG-5724 
        1.02         0.99         5.98         0.95        70.06        12.03 
TCGA-CG-5730 TCGA-CG-5732 TCGA-CG-5734 TCGA-D7-5577 TCGA-D7-6518 TCGA-D7-6519 
        4.01        55.04         7.99         8.65         9.80        15.65 
TCGA-D7-6521 TCGA-D7-6522 TCGA-D7-6525 TCGA-D7-6527 TCGA-D7-6528 TCGA-D7-6815 
        8.19         6.90         5.95         4.14         1.68         3.65 
TCGA-D7-6820 TCGA-EQ-8122 TCGA-F1-6177 TCGA-F1-6874 TCGA-F1-6875 TCGA-FP-7735 
        2.93         7.79         6.54         2.01        72.23         0.39 
TCGA-FP-7916 TCGA-FP-7998 TCGA-FP-8099 TCGA-FP-8209 TCGA-FP-8210 TCGA-FP-8631 
        3.02         3.58         1.02        59.05         5.03         0.56 
TCGA-HJ-7597 TCGA-IN-7806 TCGA-IP-7968 
       26.43         6.87         2.53 

      8P GAIN CNV 8P GAIN WILD-TYPE 
             0.13              0.07 
      8P GAIN CNV 8P GAIN WILD-TYPE 
            65.10             72.23 
      8P GAIN CNV 8P GAIN WILD-TYPE 
            4.155             1.020 
[1] "0.1 - 65.1 (4.2)" "0.1 - 72.2 (1.0)"
       TCGA-B7-5816        TCGA-B7-5818        TCGA-BR-6452        TCGA-BR-6455 
      "8P GAIN CNV" "8P GAIN WILD-TYPE"       "8P GAIN CNV"       "8P GAIN CNV" 
       TCGA-BR-6457        TCGA-BR-6458        TCGA-BR-6563        TCGA-BR-6564 
"8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" 
       TCGA-BR-6565        TCGA-BR-6566        TCGA-BR-6705        TCGA-BR-6706 
"8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" 
       TCGA-BR-6707        TCGA-BR-6709        TCGA-BR-6710        TCGA-BR-6801 
      "8P GAIN CNV" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" 
       TCGA-BR-6802        TCGA-BR-6803        TCGA-BR-6852        TCGA-BR-7196 
"8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE"       "8P GAIN CNV" "8P GAIN WILD-TYPE" 
       TCGA-BR-7197        TCGA-BR-7703        TCGA-BR-7704        TCGA-BR-7707 
"8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE"       "8P GAIN CNV"       "8P GAIN CNV" 
       TCGA-BR-7715        TCGA-BR-7716        TCGA-BR-7717        TCGA-BR-7722 
      "8P GAIN CNV" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" 
       TCGA-BR-7723        TCGA-BR-7851        TCGA-BR-7901        TCGA-BR-7957 
"8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" 
       TCGA-BR-7958        TCGA-BR-7959        TCGA-BR-8059        TCGA-BR-8060 
"8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" 
       TCGA-BR-8077        TCGA-BR-8078        TCGA-BR-8080        TCGA-BR-8081 
"8P GAIN WILD-TYPE"       "8P GAIN CNV"       "8P GAIN CNV" "8P GAIN WILD-TYPE" 
       TCGA-BR-8284        TCGA-BR-8285        TCGA-BR-8286        TCGA-BR-8289 
      "8P GAIN CNV" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" 
       TCGA-BR-8291        TCGA-BR-8295        TCGA-BR-8296        TCGA-BR-8297 
"8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE"       "8P GAIN CNV" 
       TCGA-BR-8592        TCGA-BR-A4IU        TCGA-BR-A4IV        TCGA-BR-A4IY 
"8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" 
       TCGA-BR-A4IZ        TCGA-BR-A4J1        TCGA-BR-A4J2        TCGA-BR-A4J4 
"8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" 
       TCGA-BR-A4J5        TCGA-BR-A4J6        TCGA-BR-A4J8        TCGA-BR-A4J9 
"8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" 
       TCGA-BR-A4PF        TCGA-BR-A4QI        TCGA-BR-A4QL        TCGA-CD-5798 
"8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE"       "8P GAIN CNV" "8P GAIN WILD-TYPE" 
       TCGA-CD-5799        TCGA-CD-5800        TCGA-CD-5801        TCGA-CD-5802 
"8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" 
       TCGA-CD-5803        TCGA-CG-4300        TCGA-CG-4301        TCGA-CG-4304 
"8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" 
       TCGA-CG-4305        TCGA-CG-4306        TCGA-CG-4436        TCGA-CG-4437 
      "8P GAIN CNV" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" 
       TCGA-CG-4438        TCGA-CG-4440        TCGA-CG-4441        TCGA-CG-4443 
"8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE"       "8P GAIN CNV" "8P GAIN WILD-TYPE" 
       TCGA-CG-4444        TCGA-CG-4449        TCGA-CG-4455        TCGA-CG-4460 
      "8P GAIN CNV" "8P GAIN WILD-TYPE"       "8P GAIN CNV"       "8P GAIN CNV" 
       TCGA-CG-4462        TCGA-CG-4465        TCGA-CG-4466        TCGA-CG-4469 
"8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE"       "8P GAIN CNV"       "8P GAIN CNV" 
       TCGA-CG-4472        TCGA-CG-4474        TCGA-CG-4477        TCGA-CG-5716 
      "8P GAIN CNV" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" 
       TCGA-CG-5717        TCGA-CG-5718        TCGA-CG-5719        TCGA-CG-5720 
"8P GAIN WILD-TYPE"       "8P GAIN CNV" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" 
       TCGA-CG-5721        TCGA-CG-5722        TCGA-CG-5723        TCGA-CG-5724 
"8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" 
       TCGA-CG-5725        TCGA-CG-5726        TCGA-CG-5727        TCGA-CG-5728 
      "8P GAIN CNV"       "8P GAIN CNV"       "8P GAIN CNV"       "8P GAIN CNV" 
       TCGA-CG-5730        TCGA-CG-5732        TCGA-CG-5733        TCGA-CG-5734 
"8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE"       "8P GAIN CNV" "8P GAIN WILD-TYPE" 
       TCGA-D7-5577        TCGA-D7-5578        TCGA-D7-5579        TCGA-D7-6518 
"8P GAIN WILD-TYPE"       "8P GAIN CNV"       "8P GAIN CNV" "8P GAIN WILD-TYPE" 
       TCGA-D7-6519        TCGA-D7-6520        TCGA-D7-6521        TCGA-D7-6522 
"8P GAIN WILD-TYPE"       "8P GAIN CNV" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" 
       TCGA-D7-6524        TCGA-D7-6525        TCGA-D7-6526        TCGA-D7-6527 
      "8P GAIN CNV" "8P GAIN WILD-TYPE"       "8P GAIN CNV" "8P GAIN WILD-TYPE" 
       TCGA-D7-6528        TCGA-D7-6815        TCGA-D7-6817        TCGA-D7-6818 
"8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE"       "8P GAIN CNV"       "8P GAIN CNV" 
       TCGA-D7-6820        TCGA-D7-6822        TCGA-EQ-5647        TCGA-EQ-8122 
"8P GAIN WILD-TYPE"       "8P GAIN CNV"       "8P GAIN CNV" "8P GAIN WILD-TYPE" 
       TCGA-F1-6177        TCGA-F1-6874        TCGA-F1-6875        TCGA-FP-7735 
"8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" 
       TCGA-FP-7829        TCGA-FP-7916        TCGA-FP-7998        TCGA-FP-8099 
      "8P GAIN CNV" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" 
       TCGA-FP-8209        TCGA-FP-8210        TCGA-FP-8631        TCGA-HJ-7597 
"8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" 
       TCGA-IN-7806        TCGA-IN-7808        TCGA-IP-7968 
"8P GAIN WILD-TYPE"       "8P GAIN CNV" "8P GAIN WILD-TYPE" 
       TCGA-B7-5816        TCGA-B7-5818        TCGA-BR-6452        TCGA-BR-6455 
      "8P GAIN CNV" "8P GAIN WILD-TYPE"       "8P GAIN CNV"       "8P GAIN CNV" 
       TCGA-BR-6457        TCGA-BR-6458        TCGA-BR-6563        TCGA-BR-6564 
"8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" 
       TCGA-BR-6565        TCGA-BR-6566        TCGA-BR-6705        TCGA-BR-6706 
"8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" 
       TCGA-BR-6707        TCGA-BR-6709        TCGA-BR-6710        TCGA-BR-6801 
      "8P GAIN CNV" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" 
       TCGA-BR-6802        TCGA-BR-6803        TCGA-BR-6852        TCGA-BR-7196 
"8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE"       "8P GAIN CNV" "8P GAIN WILD-TYPE" 
       TCGA-BR-7197        TCGA-BR-7703        TCGA-BR-7704        TCGA-BR-7707 
"8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE"       "8P GAIN CNV"       "8P GAIN CNV" 
       TCGA-BR-7715        TCGA-BR-7716        TCGA-BR-7717        TCGA-BR-7722 
      "8P GAIN CNV" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" 
       TCGA-BR-7723        TCGA-BR-7851        TCGA-BR-7901        TCGA-BR-7957 
"8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" 
       TCGA-BR-7958        TCGA-BR-7959        TCGA-BR-8059        TCGA-BR-8060 
"8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" 
       TCGA-BR-8077        TCGA-BR-8078        TCGA-BR-8080        TCGA-BR-8081 
"8P GAIN WILD-TYPE"       "8P GAIN CNV"       "8P GAIN CNV" "8P GAIN WILD-TYPE" 
       TCGA-BR-8284        TCGA-BR-8285        TCGA-BR-8286        TCGA-BR-8289 
      "8P GAIN CNV" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" 
       TCGA-BR-8291        TCGA-BR-8295        TCGA-BR-8296        TCGA-BR-8297 
"8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE"       "8P GAIN CNV" 
       TCGA-BR-8592        TCGA-BR-A4IU        TCGA-BR-A4IV        TCGA-BR-A4IY 
"8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" 
       TCGA-BR-A4IZ        TCGA-BR-A4J1        TCGA-BR-A4J2        TCGA-BR-A4J4 
"8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" 
       TCGA-BR-A4J5        TCGA-BR-A4J6        TCGA-BR-A4J8        TCGA-BR-A4J9 
"8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" 
       TCGA-BR-A4PF        TCGA-BR-A4QI        TCGA-BR-A4QL        TCGA-CD-5798 
"8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE"       "8P GAIN CNV" "8P GAIN WILD-TYPE" 
       TCGA-CD-5799        TCGA-CD-5800        TCGA-CD-5801        TCGA-CD-5802 
"8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" 
       TCGA-CD-5803        TCGA-CG-4300        TCGA-CG-4301        TCGA-CG-4304 
"8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" 
       TCGA-CG-4305        TCGA-CG-4306        TCGA-CG-4436        TCGA-CG-4437 
      "8P GAIN CNV" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" 
       TCGA-CG-4438        TCGA-CG-4440        TCGA-CG-4441        TCGA-CG-4443 
"8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE"       "8P GAIN CNV" "8P GAIN WILD-TYPE" 
       TCGA-CG-4444        TCGA-CG-4449        TCGA-CG-4455        TCGA-CG-4460 
      "8P GAIN CNV" "8P GAIN WILD-TYPE"       "8P GAIN CNV"       "8P GAIN CNV" 
       TCGA-CG-4462        TCGA-CG-4465        TCGA-CG-4466        TCGA-CG-4469 
"8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE"       "8P GAIN CNV"       "8P GAIN CNV" 
       TCGA-CG-4472        TCGA-CG-4474        TCGA-CG-4477        TCGA-CG-5716 
      "8P GAIN CNV" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" 
       TCGA-CG-5717        TCGA-CG-5718        TCGA-CG-5719        TCGA-CG-5720 
"8P GAIN WILD-TYPE"       "8P GAIN CNV" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" 
       TCGA-CG-5721        TCGA-CG-5722        TCGA-CG-5723        TCGA-CG-5724 
"8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" 
       TCGA-CG-5725        TCGA-CG-5726        TCGA-CG-5727        TCGA-CG-5728 
      "8P GAIN CNV"       "8P GAIN CNV"       "8P GAIN CNV"       "8P GAIN CNV" 
       TCGA-CG-5730        TCGA-CG-5732        TCGA-CG-5733        TCGA-CG-5734 
"8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE"       "8P GAIN CNV" "8P GAIN WILD-TYPE" 
       TCGA-D7-5577        TCGA-D7-5578        TCGA-D7-5579        TCGA-D7-6518 
"8P GAIN WILD-TYPE"       "8P GAIN CNV"       "8P GAIN CNV" "8P GAIN WILD-TYPE" 
       TCGA-D7-6519        TCGA-D7-6520        TCGA-D7-6521        TCGA-D7-6522 
"8P GAIN WILD-TYPE"       "8P GAIN CNV" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" 
       TCGA-D7-6524        TCGA-D7-6525        TCGA-D7-6526        TCGA-D7-6527 
      "8P GAIN CNV" "8P GAIN WILD-TYPE"       "8P GAIN CNV" "8P GAIN WILD-TYPE" 
       TCGA-D7-6528        TCGA-D7-6815        TCGA-D7-6817        TCGA-D7-6818 
"8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE"       "8P GAIN CNV"       "8P GAIN CNV" 
       TCGA-D7-6820        TCGA-D7-6822        TCGA-EQ-5647        TCGA-EQ-8122 
"8P GAIN WILD-TYPE"       "8P GAIN CNV"       "8P GAIN CNV" "8P GAIN WILD-TYPE" 
       TCGA-F1-6177        TCGA-F1-6874        TCGA-F1-6875        TCGA-FP-7735 
"8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" 
       TCGA-FP-7829        TCGA-FP-7916        TCGA-FP-7998        TCGA-FP-8099 
      "8P GAIN CNV" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" 
       TCGA-FP-8209        TCGA-FP-8210        TCGA-FP-8631        TCGA-HJ-7597 
"8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" 
       TCGA-IN-7806        TCGA-IN-7808        TCGA-IP-7968 
"8P GAIN WILD-TYPE"       "8P GAIN CNV" "8P GAIN WILD-TYPE" 
       TCGA-B7-5816        TCGA-B7-5818        TCGA-BR-6452        TCGA-BR-6455 
      "8P GAIN CNV" "8P GAIN WILD-TYPE"       "8P GAIN CNV"       "8P GAIN CNV" 
       TCGA-BR-6457        TCGA-BR-6458        TCGA-BR-6563        TCGA-BR-6564 
"8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" 
       TCGA-BR-6565        TCGA-BR-6566        TCGA-BR-6705        TCGA-BR-6706 
"8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" 
       TCGA-BR-6707        TCGA-BR-6709        TCGA-BR-6710        TCGA-BR-6801 
      "8P GAIN CNV" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" 
       TCGA-BR-6802        TCGA-BR-6803        TCGA-BR-6852        TCGA-BR-7196 
"8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE"       "8P GAIN CNV" "8P GAIN WILD-TYPE" 
       TCGA-BR-7197        TCGA-BR-7703        TCGA-BR-7704        TCGA-BR-7707 
"8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE"       "8P GAIN CNV"       "8P GAIN CNV" 
       TCGA-BR-7715        TCGA-BR-7716        TCGA-BR-7717        TCGA-BR-7722 
      "8P GAIN CNV" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" 
       TCGA-BR-7723        TCGA-BR-7851        TCGA-BR-7901        TCGA-BR-7957 
"8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" 
       TCGA-BR-7958        TCGA-BR-7959        TCGA-BR-8059        TCGA-BR-8060 
"8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" 
       TCGA-BR-8077        TCGA-BR-8078        TCGA-BR-8080        TCGA-BR-8081 
"8P GAIN WILD-TYPE"       "8P GAIN CNV"       "8P GAIN CNV" "8P GAIN WILD-TYPE" 
       TCGA-BR-8284        TCGA-BR-8285        TCGA-BR-8286        TCGA-BR-8289 
      "8P GAIN CNV" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" 
       TCGA-BR-8291        TCGA-BR-8295        TCGA-BR-8296        TCGA-BR-8297 
"8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE"       "8P GAIN CNV" 
       TCGA-BR-8592        TCGA-BR-A4IU        TCGA-BR-A4IV        TCGA-BR-A4IY 
"8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" 
       TCGA-BR-A4IZ        TCGA-BR-A4J1        TCGA-BR-A4J2        TCGA-BR-A4J4 
"8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" 
       TCGA-BR-A4J5        TCGA-BR-A4J6        TCGA-BR-A4J8        TCGA-BR-A4J9 
"8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" 
       TCGA-BR-A4PF        TCGA-BR-A4QI        TCGA-BR-A4QL        TCGA-CD-5798 
"8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE"       "8P GAIN CNV" "8P GAIN WILD-TYPE" 
       TCGA-CD-5799        TCGA-CD-5800        TCGA-CD-5801        TCGA-CD-5802 
"8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" 
       TCGA-CD-5803        TCGA-CG-4300        TCGA-CG-4301        TCGA-CG-4304 
"8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" 
       TCGA-CG-4305        TCGA-CG-4306        TCGA-CG-4436        TCGA-CG-4437 
      "8P GAIN CNV" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" 
       TCGA-CG-4438        TCGA-CG-4440        TCGA-CG-4441        TCGA-CG-4443 
"8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE"       "8P GAIN CNV" "8P GAIN WILD-TYPE" 
       TCGA-CG-4444        TCGA-CG-4449        TCGA-CG-4455        TCGA-CG-4460 
      "8P GAIN CNV" "8P GAIN WILD-TYPE"       "8P GAIN CNV"       "8P GAIN CNV" 
       TCGA-CG-4462        TCGA-CG-4465        TCGA-CG-4466        TCGA-CG-4469 
"8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE"       "8P GAIN CNV"       "8P GAIN CNV" 
       TCGA-CG-4472        TCGA-CG-4474        TCGA-CG-4477        TCGA-CG-5716 
      "8P GAIN CNV" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" 
       TCGA-CG-5717        TCGA-CG-5718        TCGA-CG-5719        TCGA-CG-5720 
"8P GAIN WILD-TYPE"       "8P GAIN CNV" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" 
       TCGA-CG-5721        TCGA-CG-5722        TCGA-CG-5723        TCGA-CG-5724 
"8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" 
       TCGA-CG-5725        TCGA-CG-5726        TCGA-CG-5727        TCGA-CG-5728 
      "8P GAIN CNV"       "8P GAIN CNV"       "8P GAIN CNV"       "8P GAIN CNV" 
       TCGA-CG-5730        TCGA-CG-5732        TCGA-CG-5733        TCGA-CG-5734 
"8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE"       "8P GAIN CNV" "8P GAIN WILD-TYPE" 
       TCGA-D7-5577        TCGA-D7-5578        TCGA-D7-5579        TCGA-D7-6518 
"8P GAIN WILD-TYPE"       "8P GAIN CNV"       "8P GAIN CNV" "8P GAIN WILD-TYPE" 
       TCGA-D7-6519        TCGA-D7-6520        TCGA-D7-6521        TCGA-D7-6522 
"8P GAIN WILD-TYPE"       "8P GAIN CNV" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" 
       TCGA-D7-6524        TCGA-D7-6525        TCGA-D7-6526        TCGA-D7-6527 
      "8P GAIN CNV" "8P GAIN WILD-TYPE"       "8P GAIN CNV" "8P GAIN WILD-TYPE" 
       TCGA-D7-6528        TCGA-D7-6815        TCGA-D7-6817        TCGA-D7-6818 
"8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE"       "8P GAIN CNV"       "8P GAIN CNV" 
       TCGA-D7-6820        TCGA-D7-6822        TCGA-EQ-5647        TCGA-EQ-8122 
"8P GAIN WILD-TYPE"       "8P GAIN CNV"       "8P GAIN CNV" "8P GAIN WILD-TYPE" 
       TCGA-F1-6177        TCGA-F1-6874        TCGA-F1-6875        TCGA-FP-7735 
"8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" 
       TCGA-FP-7829        TCGA-FP-7916        TCGA-FP-7998        TCGA-FP-8099 
      "8P GAIN CNV" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" 
       TCGA-FP-8209        TCGA-FP-8210        TCGA-FP-8631        TCGA-HJ-7597 
"8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" 
       TCGA-IN-7806        TCGA-IN-7808        TCGA-IP-7968 
"8P GAIN WILD-TYPE"       "8P GAIN CNV" "8P GAIN WILD-TYPE" 
[1] "hr=" "1.1"
D14V2, continuous
D14V3, binary
[1] "tbl2"
                   cls
clus                [,1] [,2]
  8P GAIN CNV         27   28
  8P GAIN WILD-TYPE   45   80
        clus
vv       8P GAIN CNV 8P GAIN WILD-TYPE
  FEMALE          27                45
  MALE            28                80
                   vv
clus                STOMACH  ADENOCARCINOMA  DIFFUSE TYPE
  8P GAIN CNV                                           1
  8P GAIN WILD-TYPE                                     9
                   vv
clus                STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  8P GAIN CNV                                                            2
  8P GAIN WILD-TYPE                                                     14
                   vv
clus                STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  8P GAIN CNV                                                                       1
  8P GAIN WILD-TYPE                                                                 7
                   vv
clus                STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE
  8P GAIN CNV                                                              1
  8P GAIN WILD-TYPE                                                        2
                   vv
clus                STOMACH ADENOCARCINOMA  SIGNET RING TYPE
  8P GAIN CNV                                              0
  8P GAIN WILD-TYPE                                        1
                   vv
clus                STOMACH ADENOCARCINOMA - DIFFUSE TYPE
  8P GAIN CNV                                           4
  8P GAIN WILD-TYPE                                    12
                   vv
clus                STOMACH ADENOCARCINOMA - NOT OTHERWISE SPECIFIED (NOS)
  8P GAIN CNV                                                           23
  8P GAIN WILD-TYPE                                                     50
                   vv
clus                STOMACH INTESTINAL ADENOCARCINOMA - MUCINOUS TYPE
  8P GAIN CNV                                                       4
  8P GAIN WILD-TYPE                                                 3
                   vv
clus                STOMACH INTESTINAL ADENOCARCINOMA - PAPILLARY TYPE
  8P GAIN CNV                                                        0
  8P GAIN WILD-TYPE                                                  3
                   vv
clus                STOMACH INTESTINAL ADENOCARCINOMA - TUBULAR TYPE
  8P GAIN CNV                                                      5
  8P GAIN WILD-TYPE                                                5
                   vv
clus                STOMACH INTESTINAL ADENOCARCINOMA - TYPE NOT OTHERWISE SPECIFIED (NOS)
  8P GAIN CNV                                                                           12
  8P GAIN WILD-TYPE                                                                     16
D14V4, multiclass
                   vv
clus                T1 T2 T3 T4
  8P GAIN CNV        3 21 15  6
  8P GAIN WILD-TYPE  3 31 41 12
D14V5, multiclass
    clus
vv   8P GAIN CNV 8P GAIN WILD-TYPE
  T1           3                 3
  T2          21                31
  T3          15                41
  T4           6                12
                   vv
clus                N0 N1 N2 N3
  8P GAIN CNV       17 13  8  5
  8P GAIN WILD-TYPE 27 36 15 10
D14V6, multiclass
    clus
vv   8P GAIN CNV 8P GAIN WILD-TYPE
  N0          17                27
  N1          13                36
  N2           8                15
  N3           5                10
                   vv
clus                M0 M1 MX
  8P GAIN CNV       46  3  1
  8P GAIN WILD-TYPE 72 13  7
D14V7, multiclass
    clus
vv   8P GAIN CNV 8P GAIN WILD-TYPE
  M0          46                72
  M1           3                13
  MX           1                 7
                   vv
clus                 I II III IV
  8P GAIN CNV        9 14  13  6
  8P GAIN WILD-TYPE 15 23  26 20
D14V8, multiclass
     clus
vv    8P GAIN CNV 8P GAIN WILD-TYPE
  I             9                15
  II           14                23
  III          13                26
  IV            6                20
D14V9, binary
[1] "tbl2"
                   cls
clus                [,1] [,2]
  8P GAIN CNV          3   52
  8P GAIN WILD-TYPE    2  123
     clus
vv    8P GAIN CNV 8P GAIN WILD-TYPE
  NO            3                 2
  YES          52               123
                   vv
clus                R0 R1 R2 RX
  8P GAIN CNV       37  3  2 12
  8P GAIN WILD-TYPE 88  4 10 13
D14V10, multiclass
    clus
vv   8P GAIN CNV 8P GAIN WILD-TYPE
  R0          37                88
  R1           3                 4
  R2           2                10
  RX          12                13
D14V11, continuous

Clustering(15) Variable = 8q gain
D15V1, survival
                   sevent
clus2                0  1
  8Q GAIN CNV       46  9
  8Q GAIN WILD-TYPE 78 10
      8Q GAIN CNV 8Q GAIN WILD-TYPE 
               55                88 
      8Q GAIN CNV 8Q GAIN WILD-TYPE 
                9                10 
$`8Q GAIN CNV`
TCGA-B7-5816 TCGA-BR-6452 TCGA-BR-6455 TCGA-BR-6565 TCGA-BR-6707 TCGA-BR-6709 
        5.62         0.95         1.41         0.62         0.99         1.22 
TCGA-BR-6852 TCGA-BR-7197 TCGA-BR-7704 TCGA-BR-7707 TCGA-BR-7715 TCGA-BR-7716 
        0.26         1.48         1.25         0.13         1.05         0.82 
TCGA-BR-8077 TCGA-BR-8078 TCGA-BR-8080 TCGA-BR-8284 TCGA-BR-8297 TCGA-BR-A4J1 
        0.69         0.95         0.49         0.72         0.76         0.72 
TCGA-BR-A4QL TCGA-CD-5800 TCGA-CG-4305 TCGA-CG-4436 TCGA-CG-4438 TCGA-CG-4441 
        2.24         0.36        15.95        52.96        54.05        14.01 
TCGA-CG-4443 TCGA-CG-4444 TCGA-CG-4455 TCGA-CG-4460 TCGA-CG-4466 TCGA-CG-4469 
       29.98        47.05        12.03        21.99        18.94         7.07 
TCGA-CG-4472 TCGA-CG-5718 TCGA-CG-5725 TCGA-CG-5726 TCGA-CG-5727 TCGA-CG-5728 
       12.00         1.02        15.02        28.96        31.04        65.10 
TCGA-CG-5733 TCGA-D7-5578 TCGA-D7-5579 TCGA-D7-6520 TCGA-D7-6524 TCGA-D7-6525 
       21.07         3.58         4.54         9.63         0.69         5.95 
TCGA-D7-6526 TCGA-D7-6815 TCGA-D7-6817 TCGA-D7-6818 TCGA-D7-6822 TCGA-EQ-5647 
        6.61         3.65         4.70         4.04         4.27         0.62 
TCGA-EQ-8122 TCGA-F1-6177 TCGA-F1-6875 TCGA-FP-7735 TCGA-FP-7829 TCGA-FP-8631 
        7.79         6.54        72.23         0.39         0.20         0.56 
TCGA-IN-7808 
        3.55 

$`8Q GAIN WILD-TYPE`
TCGA-B7-5818 TCGA-BR-6457 TCGA-BR-6458 TCGA-BR-6563 TCGA-BR-6564 TCGA-BR-6566 
        0.10         1.35         1.35         0.85         0.82         0.62 
TCGA-BR-6705 TCGA-BR-6706 TCGA-BR-6710 TCGA-BR-6801 TCGA-BR-6802 TCGA-BR-6803 
        1.71         2.17         0.66         1.12         0.76         0.66 
TCGA-BR-7196 TCGA-BR-7703 TCGA-BR-7717 TCGA-BR-7722 TCGA-BR-7723 TCGA-BR-7851 
        1.22         0.46         0.69         0.16         4.54         0.99 
TCGA-BR-7901 TCGA-BR-7957 TCGA-BR-7958 TCGA-BR-7959 TCGA-BR-8059 TCGA-BR-8060 
        0.95         0.69         0.16         1.08         0.82         1.32 
TCGA-BR-8081 TCGA-BR-8285 TCGA-BR-8286 TCGA-BR-8289 TCGA-BR-8291 TCGA-BR-8295 
        0.46         0.26         0.43         0.26         1.18         1.55 
TCGA-BR-8296 TCGA-BR-8592 TCGA-BR-A4IU TCGA-BR-A4IV TCGA-BR-A4IY TCGA-BR-A4IZ 
        1.48         0.20         0.59         0.92         0.39         0.79 
TCGA-BR-A4J2 TCGA-BR-A4J4 TCGA-BR-A4J5 TCGA-BR-A4J6 TCGA-BR-A4J8 TCGA-BR-A4J9 
        0.79         0.53         0.43         0.13         0.23         0.10 
TCGA-BR-A4PF TCGA-BR-A4QI TCGA-CD-5798 TCGA-CD-5799 TCGA-CD-5801 TCGA-CD-5802 
        0.72         0.49         0.82         0.69         0.49         0.30 
TCGA-CD-5803 TCGA-CG-4300 TCGA-CG-4301 TCGA-CG-4304 TCGA-CG-4306 TCGA-CG-4437 
        0.07        20.02         3.02        27.02         1.02         8.05 
TCGA-CG-4440 TCGA-CG-4449 TCGA-CG-4462 TCGA-CG-4465 TCGA-CG-4474 TCGA-CG-4477 
        4.01        19.07         1.02         8.98         1.02         1.02 
TCGA-CG-5716 TCGA-CG-5717 TCGA-CG-5719 TCGA-CG-5720 TCGA-CG-5721 TCGA-CG-5722 
        1.02         6.94         1.02         0.99         5.98         0.95 
TCGA-CG-5723 TCGA-CG-5724 TCGA-CG-5730 TCGA-CG-5732 TCGA-CG-5734 TCGA-D7-5577 
       70.06        12.03         4.01        55.04         7.99         8.65 
TCGA-D7-6518 TCGA-D7-6519 TCGA-D7-6521 TCGA-D7-6522 TCGA-D7-6527 TCGA-D7-6528 
        9.80        15.65         8.19         6.90         4.14         1.68 
TCGA-D7-6820 TCGA-F1-6874 TCGA-FP-7916 TCGA-FP-7998 TCGA-FP-8099 TCGA-FP-8209 
        2.93         2.01         3.02         3.58         1.02        59.05 
TCGA-FP-8210 TCGA-HJ-7597 TCGA-IN-7806 TCGA-IP-7968 
        5.03        26.43         6.87         2.53 

      8Q GAIN CNV 8Q GAIN WILD-TYPE 
             0.13              0.07 
      8Q GAIN CNV 8Q GAIN WILD-TYPE 
            72.23             70.06 
      8Q GAIN CNV 8Q GAIN WILD-TYPE 
             3.65              1.02 
[1] "0.1 - 72.2 (3.6)" "0.1 - 70.1 (1.0)"
       TCGA-B7-5816        TCGA-B7-5818        TCGA-BR-6452        TCGA-BR-6455 
      "8Q GAIN CNV" "8Q GAIN WILD-TYPE"       "8Q GAIN CNV"       "8Q GAIN CNV" 
       TCGA-BR-6457        TCGA-BR-6458        TCGA-BR-6563        TCGA-BR-6564 
"8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE" 
       TCGA-BR-6565        TCGA-BR-6566        TCGA-BR-6705        TCGA-BR-6706 
      "8Q GAIN CNV" "8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE" 
       TCGA-BR-6707        TCGA-BR-6709        TCGA-BR-6710        TCGA-BR-6801 
      "8Q GAIN CNV"       "8Q GAIN CNV" "8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE" 
       TCGA-BR-6802        TCGA-BR-6803        TCGA-BR-6852        TCGA-BR-7196 
"8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE"       "8Q GAIN CNV" "8Q GAIN WILD-TYPE" 
       TCGA-BR-7197        TCGA-BR-7703        TCGA-BR-7704        TCGA-BR-7707 
      "8Q GAIN CNV" "8Q GAIN WILD-TYPE"       "8Q GAIN CNV"       "8Q GAIN CNV" 
       TCGA-BR-7715        TCGA-BR-7716        TCGA-BR-7717        TCGA-BR-7722 
      "8Q GAIN CNV"       "8Q GAIN CNV" "8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE" 
       TCGA-BR-7723        TCGA-BR-7851        TCGA-BR-7901        TCGA-BR-7957 
"8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE" 
       TCGA-BR-7958        TCGA-BR-7959        TCGA-BR-8059        TCGA-BR-8060 
"8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE" 
       TCGA-BR-8077        TCGA-BR-8078        TCGA-BR-8080        TCGA-BR-8081 
      "8Q GAIN CNV"       "8Q GAIN CNV"       "8Q GAIN CNV" "8Q GAIN WILD-TYPE" 
       TCGA-BR-8284        TCGA-BR-8285        TCGA-BR-8286        TCGA-BR-8289 
      "8Q GAIN CNV" "8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE" 
       TCGA-BR-8291        TCGA-BR-8295        TCGA-BR-8296        TCGA-BR-8297 
"8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE"       "8Q GAIN CNV" 
       TCGA-BR-8592        TCGA-BR-A4IU        TCGA-BR-A4IV        TCGA-BR-A4IY 
"8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE" 
       TCGA-BR-A4IZ        TCGA-BR-A4J1        TCGA-BR-A4J2        TCGA-BR-A4J4 
"8Q GAIN WILD-TYPE"       "8Q GAIN CNV" "8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE" 
       TCGA-BR-A4J5        TCGA-BR-A4J6        TCGA-BR-A4J8        TCGA-BR-A4J9 
"8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE" 
       TCGA-BR-A4PF        TCGA-BR-A4QI        TCGA-BR-A4QL        TCGA-CD-5798 
"8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE"       "8Q GAIN CNV" "8Q GAIN WILD-TYPE" 
       TCGA-CD-5799        TCGA-CD-5800        TCGA-CD-5801        TCGA-CD-5802 
"8Q GAIN WILD-TYPE"       "8Q GAIN CNV" "8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE" 
       TCGA-CD-5803        TCGA-CG-4300        TCGA-CG-4301        TCGA-CG-4304 
"8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE" 
       TCGA-CG-4305        TCGA-CG-4306        TCGA-CG-4436        TCGA-CG-4437 
      "8Q GAIN CNV" "8Q GAIN WILD-TYPE"       "8Q GAIN CNV" "8Q GAIN WILD-TYPE" 
       TCGA-CG-4438        TCGA-CG-4440        TCGA-CG-4441        TCGA-CG-4443 
      "8Q GAIN CNV" "8Q GAIN WILD-TYPE"       "8Q GAIN CNV"       "8Q GAIN CNV" 
       TCGA-CG-4444        TCGA-CG-4449        TCGA-CG-4455        TCGA-CG-4460 
      "8Q GAIN CNV" "8Q GAIN WILD-TYPE"       "8Q GAIN CNV"       "8Q GAIN CNV" 
       TCGA-CG-4462        TCGA-CG-4465        TCGA-CG-4466        TCGA-CG-4469 
"8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE"       "8Q GAIN CNV"       "8Q GAIN CNV" 
       TCGA-CG-4472        TCGA-CG-4474        TCGA-CG-4477        TCGA-CG-5716 
      "8Q GAIN CNV" "8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE" 
       TCGA-CG-5717        TCGA-CG-5718        TCGA-CG-5719        TCGA-CG-5720 
"8Q GAIN WILD-TYPE"       "8Q GAIN CNV" "8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE" 
       TCGA-CG-5721        TCGA-CG-5722        TCGA-CG-5723        TCGA-CG-5724 
"8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE" 
       TCGA-CG-5725        TCGA-CG-5726        TCGA-CG-5727        TCGA-CG-5728 
      "8Q GAIN CNV"       "8Q GAIN CNV"       "8Q GAIN CNV"       "8Q GAIN CNV" 
       TCGA-CG-5730        TCGA-CG-5732        TCGA-CG-5733        TCGA-CG-5734 
"8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE"       "8Q GAIN CNV" "8Q GAIN WILD-TYPE" 
       TCGA-D7-5577        TCGA-D7-5578        TCGA-D7-5579        TCGA-D7-6518 
"8Q GAIN WILD-TYPE"       "8Q GAIN CNV"       "8Q GAIN CNV" "8Q GAIN WILD-TYPE" 
       TCGA-D7-6519        TCGA-D7-6520        TCGA-D7-6521        TCGA-D7-6522 
"8Q GAIN WILD-TYPE"       "8Q GAIN CNV" "8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE" 
       TCGA-D7-6524        TCGA-D7-6525        TCGA-D7-6526        TCGA-D7-6527 
      "8Q GAIN CNV"       "8Q GAIN CNV"       "8Q GAIN CNV" "8Q GAIN WILD-TYPE" 
       TCGA-D7-6528        TCGA-D7-6815        TCGA-D7-6817        TCGA-D7-6818 
"8Q GAIN WILD-TYPE"       "8Q GAIN CNV"       "8Q GAIN CNV"       "8Q GAIN CNV" 
       TCGA-D7-6820        TCGA-D7-6822        TCGA-EQ-5647        TCGA-EQ-8122 
"8Q GAIN WILD-TYPE"       "8Q GAIN CNV"       "8Q GAIN CNV"       "8Q GAIN CNV" 
       TCGA-F1-6177        TCGA-F1-6874        TCGA-F1-6875        TCGA-FP-7735 
      "8Q GAIN CNV" "8Q GAIN WILD-TYPE"       "8Q GAIN CNV"       "8Q GAIN CNV" 
       TCGA-FP-7829        TCGA-FP-7916        TCGA-FP-7998        TCGA-FP-8099 
      "8Q GAIN CNV" "8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE" 
       TCGA-FP-8209        TCGA-FP-8210        TCGA-FP-8631        TCGA-HJ-7597 
"8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE"       "8Q GAIN CNV" "8Q GAIN WILD-TYPE" 
       TCGA-IN-7806        TCGA-IN-7808        TCGA-IP-7968 
"8Q GAIN WILD-TYPE"       "8Q GAIN CNV" "8Q GAIN WILD-TYPE" 
       TCGA-B7-5816        TCGA-B7-5818        TCGA-BR-6452        TCGA-BR-6455 
      "8Q GAIN CNV" "8Q GAIN WILD-TYPE"       "8Q GAIN CNV"       "8Q GAIN CNV" 
       TCGA-BR-6457        TCGA-BR-6458        TCGA-BR-6563        TCGA-BR-6564 
"8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE" 
       TCGA-BR-6565        TCGA-BR-6566        TCGA-BR-6705        TCGA-BR-6706 
      "8Q GAIN CNV" "8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE" 
       TCGA-BR-6707        TCGA-BR-6709        TCGA-BR-6710        TCGA-BR-6801 
      "8Q GAIN CNV"       "8Q GAIN CNV" "8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE" 
       TCGA-BR-6802        TCGA-BR-6803        TCGA-BR-6852        TCGA-BR-7196 
"8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE"       "8Q GAIN CNV" "8Q GAIN WILD-TYPE" 
       TCGA-BR-7197        TCGA-BR-7703        TCGA-BR-7704        TCGA-BR-7707 
      "8Q GAIN CNV" "8Q GAIN WILD-TYPE"       "8Q GAIN CNV"       "8Q GAIN CNV" 
       TCGA-BR-7715        TCGA-BR-7716        TCGA-BR-7717        TCGA-BR-7722 
      "8Q GAIN CNV"       "8Q GAIN CNV" "8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE" 
       TCGA-BR-7723        TCGA-BR-7851        TCGA-BR-7901        TCGA-BR-7957 
"8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE" 
       TCGA-BR-7958        TCGA-BR-7959        TCGA-BR-8059        TCGA-BR-8060 
"8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE" 
       TCGA-BR-8077        TCGA-BR-8078        TCGA-BR-8080        TCGA-BR-8081 
      "8Q GAIN CNV"       "8Q GAIN CNV"       "8Q GAIN CNV" "8Q GAIN WILD-TYPE" 
       TCGA-BR-8284        TCGA-BR-8285        TCGA-BR-8286        TCGA-BR-8289 
      "8Q GAIN CNV" "8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE" 
       TCGA-BR-8291        TCGA-BR-8295        TCGA-BR-8296        TCGA-BR-8297 
"8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE"       "8Q GAIN CNV" 
       TCGA-BR-8592        TCGA-BR-A4IU        TCGA-BR-A4IV        TCGA-BR-A4IY 
"8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE" 
       TCGA-BR-A4IZ        TCGA-BR-A4J1        TCGA-BR-A4J2        TCGA-BR-A4J4 
"8Q GAIN WILD-TYPE"       "8Q GAIN CNV" "8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE" 
       TCGA-BR-A4J5        TCGA-BR-A4J6        TCGA-BR-A4J8        TCGA-BR-A4J9 
"8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE" 
       TCGA-BR-A4PF        TCGA-BR-A4QI        TCGA-BR-A4QL        TCGA-CD-5798 
"8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE"       "8Q GAIN CNV" "8Q GAIN WILD-TYPE" 
       TCGA-CD-5799        TCGA-CD-5800        TCGA-CD-5801        TCGA-CD-5802 
"8Q GAIN WILD-TYPE"       "8Q GAIN CNV" "8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE" 
       TCGA-CD-5803        TCGA-CG-4300        TCGA-CG-4301        TCGA-CG-4304 
"8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE" 
       TCGA-CG-4305        TCGA-CG-4306        TCGA-CG-4436        TCGA-CG-4437 
      "8Q GAIN CNV" "8Q GAIN WILD-TYPE"       "8Q GAIN CNV" "8Q GAIN WILD-TYPE" 
       TCGA-CG-4438        TCGA-CG-4440        TCGA-CG-4441        TCGA-CG-4443 
      "8Q GAIN CNV" "8Q GAIN WILD-TYPE"       "8Q GAIN CNV"       "8Q GAIN CNV" 
       TCGA-CG-4444        TCGA-CG-4449        TCGA-CG-4455        TCGA-CG-4460 
      "8Q GAIN CNV" "8Q GAIN WILD-TYPE"       "8Q GAIN CNV"       "8Q GAIN CNV" 
       TCGA-CG-4462        TCGA-CG-4465        TCGA-CG-4466        TCGA-CG-4469 
"8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE"       "8Q GAIN CNV"       "8Q GAIN CNV" 
       TCGA-CG-4472        TCGA-CG-4474        TCGA-CG-4477        TCGA-CG-5716 
      "8Q GAIN CNV" "8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE" 
       TCGA-CG-5717        TCGA-CG-5718        TCGA-CG-5719        TCGA-CG-5720 
"8Q GAIN WILD-TYPE"       "8Q GAIN CNV" "8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE" 
       TCGA-CG-5721        TCGA-CG-5722        TCGA-CG-5723        TCGA-CG-5724 
"8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE" 
       TCGA-CG-5725        TCGA-CG-5726        TCGA-CG-5727        TCGA-CG-5728 
      "8Q GAIN CNV"       "8Q GAIN CNV"       "8Q GAIN CNV"       "8Q GAIN CNV" 
       TCGA-CG-5730        TCGA-CG-5732        TCGA-CG-5733        TCGA-CG-5734 
"8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE"       "8Q GAIN CNV" "8Q GAIN WILD-TYPE" 
       TCGA-D7-5577        TCGA-D7-5578        TCGA-D7-5579        TCGA-D7-6518 
"8Q GAIN WILD-TYPE"       "8Q GAIN CNV"       "8Q GAIN CNV" "8Q GAIN WILD-TYPE" 
       TCGA-D7-6519        TCGA-D7-6520        TCGA-D7-6521        TCGA-D7-6522 
"8Q GAIN WILD-TYPE"       "8Q GAIN CNV" "8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE" 
       TCGA-D7-6524        TCGA-D7-6525        TCGA-D7-6526        TCGA-D7-6527 
      "8Q GAIN CNV"       "8Q GAIN CNV"       "8Q GAIN CNV" "8Q GAIN WILD-TYPE" 
       TCGA-D7-6528        TCGA-D7-6815        TCGA-D7-6817        TCGA-D7-6818 
"8Q GAIN WILD-TYPE"       "8Q GAIN CNV"       "8Q GAIN CNV"       "8Q GAIN CNV" 
       TCGA-D7-6820        TCGA-D7-6822        TCGA-EQ-5647        TCGA-EQ-8122 
"8Q GAIN WILD-TYPE"       "8Q GAIN CNV"       "8Q GAIN CNV"       "8Q GAIN CNV" 
       TCGA-F1-6177        TCGA-F1-6874        TCGA-F1-6875        TCGA-FP-7735 
      "8Q GAIN CNV" "8Q GAIN WILD-TYPE"       "8Q GAIN CNV"       "8Q GAIN CNV" 
       TCGA-FP-7829        TCGA-FP-7916        TCGA-FP-7998        TCGA-FP-8099 
      "8Q GAIN CNV" "8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE" 
       TCGA-FP-8209        TCGA-FP-8210        TCGA-FP-8631        TCGA-HJ-7597 
"8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE"       "8Q GAIN CNV" "8Q GAIN WILD-TYPE" 
       TCGA-IN-7806        TCGA-IN-7808        TCGA-IP-7968 
"8Q GAIN WILD-TYPE"       "8Q GAIN CNV" "8Q GAIN WILD-TYPE" 
       TCGA-B7-5816        TCGA-B7-5818        TCGA-BR-6452        TCGA-BR-6455 
      "8Q GAIN CNV" "8Q GAIN WILD-TYPE"       "8Q GAIN CNV"       "8Q GAIN CNV" 
       TCGA-BR-6457        TCGA-BR-6458        TCGA-BR-6563        TCGA-BR-6564 
"8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE" 
       TCGA-BR-6565        TCGA-BR-6566        TCGA-BR-6705        TCGA-BR-6706 
      "8Q GAIN CNV" "8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE" 
       TCGA-BR-6707        TCGA-BR-6709        TCGA-BR-6710        TCGA-BR-6801 
      "8Q GAIN CNV"       "8Q GAIN CNV" "8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE" 
       TCGA-BR-6802        TCGA-BR-6803        TCGA-BR-6852        TCGA-BR-7196 
"8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE"       "8Q GAIN CNV" "8Q GAIN WILD-TYPE" 
       TCGA-BR-7197        TCGA-BR-7703        TCGA-BR-7704        TCGA-BR-7707 
      "8Q GAIN CNV" "8Q GAIN WILD-TYPE"       "8Q GAIN CNV"       "8Q GAIN CNV" 
       TCGA-BR-7715        TCGA-BR-7716        TCGA-BR-7717        TCGA-BR-7722 
      "8Q GAIN CNV"       "8Q GAIN CNV" "8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE" 
       TCGA-BR-7723        TCGA-BR-7851        TCGA-BR-7901        TCGA-BR-7957 
"8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE" 
       TCGA-BR-7958        TCGA-BR-7959        TCGA-BR-8059        TCGA-BR-8060 
"8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE" 
       TCGA-BR-8077        TCGA-BR-8078        TCGA-BR-8080        TCGA-BR-8081 
      "8Q GAIN CNV"       "8Q GAIN CNV"       "8Q GAIN CNV" "8Q GAIN WILD-TYPE" 
       TCGA-BR-8284        TCGA-BR-8285        TCGA-BR-8286        TCGA-BR-8289 
      "8Q GAIN CNV" "8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE" 
       TCGA-BR-8291        TCGA-BR-8295        TCGA-BR-8296        TCGA-BR-8297 
"8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE"       "8Q GAIN CNV" 
       TCGA-BR-8592        TCGA-BR-A4IU        TCGA-BR-A4IV        TCGA-BR-A4IY 
"8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE" 
       TCGA-BR-A4IZ        TCGA-BR-A4J1        TCGA-BR-A4J2        TCGA-BR-A4J4 
"8Q GAIN WILD-TYPE"       "8Q GAIN CNV" "8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE" 
       TCGA-BR-A4J5        TCGA-BR-A4J6        TCGA-BR-A4J8        TCGA-BR-A4J9 
"8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE" 
       TCGA-BR-A4PF        TCGA-BR-A4QI        TCGA-BR-A4QL        TCGA-CD-5798 
"8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE"       "8Q GAIN CNV" "8Q GAIN WILD-TYPE" 
       TCGA-CD-5799        TCGA-CD-5800        TCGA-CD-5801        TCGA-CD-5802 
"8Q GAIN WILD-TYPE"       "8Q GAIN CNV" "8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE" 
       TCGA-CD-5803        TCGA-CG-4300        TCGA-CG-4301        TCGA-CG-4304 
"8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE" 
       TCGA-CG-4305        TCGA-CG-4306        TCGA-CG-4436        TCGA-CG-4437 
      "8Q GAIN CNV" "8Q GAIN WILD-TYPE"       "8Q GAIN CNV" "8Q GAIN WILD-TYPE" 
       TCGA-CG-4438        TCGA-CG-4440        TCGA-CG-4441        TCGA-CG-4443 
      "8Q GAIN CNV" "8Q GAIN WILD-TYPE"       "8Q GAIN CNV"       "8Q GAIN CNV" 
       TCGA-CG-4444        TCGA-CG-4449        TCGA-CG-4455        TCGA-CG-4460 
      "8Q GAIN CNV" "8Q GAIN WILD-TYPE"       "8Q GAIN CNV"       "8Q GAIN CNV" 
       TCGA-CG-4462        TCGA-CG-4465        TCGA-CG-4466        TCGA-CG-4469 
"8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE"       "8Q GAIN CNV"       "8Q GAIN CNV" 
       TCGA-CG-4472        TCGA-CG-4474        TCGA-CG-4477        TCGA-CG-5716 
      "8Q GAIN CNV" "8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE" 
       TCGA-CG-5717        TCGA-CG-5718        TCGA-CG-5719        TCGA-CG-5720 
"8Q GAIN WILD-TYPE"       "8Q GAIN CNV" "8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE" 
       TCGA-CG-5721        TCGA-CG-5722        TCGA-CG-5723        TCGA-CG-5724 
"8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE" 
       TCGA-CG-5725        TCGA-CG-5726        TCGA-CG-5727        TCGA-CG-5728 
      "8Q GAIN CNV"       "8Q GAIN CNV"       "8Q GAIN CNV"       "8Q GAIN CNV" 
       TCGA-CG-5730        TCGA-CG-5732        TCGA-CG-5733        TCGA-CG-5734 
"8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE"       "8Q GAIN CNV" "8Q GAIN WILD-TYPE" 
       TCGA-D7-5577        TCGA-D7-5578        TCGA-D7-5579        TCGA-D7-6518 
"8Q GAIN WILD-TYPE"       "8Q GAIN CNV"       "8Q GAIN CNV" "8Q GAIN WILD-TYPE" 
       TCGA-D7-6519        TCGA-D7-6520        TCGA-D7-6521        TCGA-D7-6522 
"8Q GAIN WILD-TYPE"       "8Q GAIN CNV" "8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE" 
       TCGA-D7-6524        TCGA-D7-6525        TCGA-D7-6526        TCGA-D7-6527 
      "8Q GAIN CNV"       "8Q GAIN CNV"       "8Q GAIN CNV" "8Q GAIN WILD-TYPE" 
       TCGA-D7-6528        TCGA-D7-6815        TCGA-D7-6817        TCGA-D7-6818 
"8Q GAIN WILD-TYPE"       "8Q GAIN CNV"       "8Q GAIN CNV"       "8Q GAIN CNV" 
       TCGA-D7-6820        TCGA-D7-6822        TCGA-EQ-5647        TCGA-EQ-8122 
"8Q GAIN WILD-TYPE"       "8Q GAIN CNV"       "8Q GAIN CNV"       "8Q GAIN CNV" 
       TCGA-F1-6177        TCGA-F1-6874        TCGA-F1-6875        TCGA-FP-7735 
      "8Q GAIN CNV" "8Q GAIN WILD-TYPE"       "8Q GAIN CNV"       "8Q GAIN CNV" 
       TCGA-FP-7829        TCGA-FP-7916        TCGA-FP-7998        TCGA-FP-8099 
      "8Q GAIN CNV" "8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE" 
       TCGA-FP-8209        TCGA-FP-8210        TCGA-FP-8631        TCGA-HJ-7597 
"8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE"       "8Q GAIN CNV" "8Q GAIN WILD-TYPE" 
       TCGA-IN-7806        TCGA-IN-7808        TCGA-IP-7968 
"8Q GAIN WILD-TYPE"       "8Q GAIN CNV" "8Q GAIN WILD-TYPE" 
[1] "hr=" "1.6"
D15V2, continuous
D15V3, binary
[1] "tbl2"
                   cls
clus                [,1] [,2]
  8Q GAIN CNV         35   41
  8Q GAIN WILD-TYPE   37   67
        clus
vv       8Q GAIN CNV 8Q GAIN WILD-TYPE
  FEMALE          35                37
  MALE            41                67
                   vv
clus                STOMACH  ADENOCARCINOMA  DIFFUSE TYPE
  8Q GAIN CNV                                           1
  8Q GAIN WILD-TYPE                                     9
                   vv
clus                STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  8Q GAIN CNV                                                            3
  8Q GAIN WILD-TYPE                                                     13
                   vv
clus                STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  8Q GAIN CNV                                                                       4
  8Q GAIN WILD-TYPE                                                                 4
                   vv
clus                STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE
  8Q GAIN CNV                                                              1
  8Q GAIN WILD-TYPE                                                        2
                   vv
clus                STOMACH ADENOCARCINOMA  SIGNET RING TYPE
  8Q GAIN CNV                                              0
  8Q GAIN WILD-TYPE                                        1
                   vv
clus                STOMACH ADENOCARCINOMA - DIFFUSE TYPE
  8Q GAIN CNV                                           5
  8Q GAIN WILD-TYPE                                    11
                   vv
clus                STOMACH ADENOCARCINOMA - NOT OTHERWISE SPECIFIED (NOS)
  8Q GAIN CNV                                                           34
  8Q GAIN WILD-TYPE                                                     39
                   vv
clus                STOMACH INTESTINAL ADENOCARCINOMA - MUCINOUS TYPE
  8Q GAIN CNV                                                       4
  8Q GAIN WILD-TYPE                                                 3
                   vv
clus                STOMACH INTESTINAL ADENOCARCINOMA - PAPILLARY TYPE
  8Q GAIN CNV                                                        1
  8Q GAIN WILD-TYPE                                                  2
                   vv
clus                STOMACH INTESTINAL ADENOCARCINOMA - TUBULAR TYPE
  8Q GAIN CNV                                                      6
  8Q GAIN WILD-TYPE                                                4
                   vv
clus                STOMACH INTESTINAL ADENOCARCINOMA - TYPE NOT OTHERWISE SPECIFIED (NOS)
  8Q GAIN CNV                                                                           15
  8Q GAIN WILD-TYPE                                                                     13
D15V4, multiclass
                   vv
clus                T1 T2 T3 T4
  8Q GAIN CNV        5 26 22  8
  8Q GAIN WILD-TYPE  1 26 34 10
D15V5, multiclass
    clus
vv   8Q GAIN CNV 8Q GAIN WILD-TYPE
  T1           5                 1
  T2          26                26
  T3          22                34
  T4           8                10
                   vv
clus                N0 N1 N2 N3
  8Q GAIN CNV       24 18 12  5
  8Q GAIN WILD-TYPE 20 31 11 10
D15V6, multiclass
    clus
vv   8Q GAIN CNV 8Q GAIN WILD-TYPE
  N0          24                20
  N1          18                31
  N2          12                11
  N3           5                10
                   vv
clus                M0 M1 MX
  8Q GAIN CNV       60  3  4
  8Q GAIN WILD-TYPE 58 13  4
D15V7, multiclass
    clus
vv   8Q GAIN CNV 8Q GAIN WILD-TYPE
  M0          60                58
  M1           3                13
  MX           4                 4
                   vv
clus                 I II III IV
  8Q GAIN CNV       14 18  17  8
  8Q GAIN WILD-TYPE 10 19  22 18
D15V8, multiclass
     clus
vv    8Q GAIN CNV 8Q GAIN WILD-TYPE
  I            14                10
  II           18                19
  III          17                22
  IV            8                18
D15V9, binary
[1] "tbl2"
                   cls
clus                [,1] [,2]
  8Q GAIN CNV          3   73
  8Q GAIN WILD-TYPE    2  102
     clus
vv    8Q GAIN CNV 8Q GAIN WILD-TYPE
  NO            3                 2
  YES          73               102
                   vv
clus                R0 R1 R2 RX
  8Q GAIN CNV       52  5  2 14
  8Q GAIN WILD-TYPE 73  2 10 11
D15V10, multiclass
    clus
vv   8Q GAIN CNV 8Q GAIN WILD-TYPE
  R0          52                73
  R1           5                 2
  R2           2                10
  RX          14                11
D15V11, continuous

Clustering(16) Variable = 9p gain
D16V1, survival
                   sevent
clus2                 0   1
  9P GAIN CNV        10   1
  9P GAIN WILD-TYPE 114  18
      9P GAIN CNV 9P GAIN WILD-TYPE 
               11               132 
      9P GAIN CNV 9P GAIN WILD-TYPE 
                1                18 
$`9P GAIN CNV`
TCGA-BR-6707 TCGA-BR-7707 TCGA-BR-8289 TCGA-BR-8295 TCGA-BR-A4J4 TCGA-BR-A4J9 
        0.99         0.13         0.26         1.55         0.53         0.10 
TCGA-CG-4436 TCGA-D7-6528 TCGA-D7-6818 TCGA-D7-6822 TCGA-EQ-5647 
       52.96         1.68         4.04         4.27         0.62 

$`9P GAIN WILD-TYPE`
TCGA-B7-5816 TCGA-B7-5818 TCGA-BR-6452 TCGA-BR-6455 TCGA-BR-6457 TCGA-BR-6458 
        5.62         0.10         0.95         1.41         1.35         1.35 
TCGA-BR-6563 TCGA-BR-6564 TCGA-BR-6565 TCGA-BR-6566 TCGA-BR-6705 TCGA-BR-6706 
        0.85         0.82         0.62         0.62         1.71         2.17 
TCGA-BR-6709 TCGA-BR-6710 TCGA-BR-6801 TCGA-BR-6802 TCGA-BR-6803 TCGA-BR-6852 
        1.22         0.66         1.12         0.76         0.66         0.26 
TCGA-BR-7196 TCGA-BR-7197 TCGA-BR-7703 TCGA-BR-7704 TCGA-BR-7715 TCGA-BR-7716 
        1.22         1.48         0.46         1.25         1.05         0.82 
TCGA-BR-7717 TCGA-BR-7722 TCGA-BR-7723 TCGA-BR-7851 TCGA-BR-7901 TCGA-BR-7957 
        0.69         0.16         4.54         0.99         0.95         0.69 
TCGA-BR-7958 TCGA-BR-7959 TCGA-BR-8059 TCGA-BR-8060 TCGA-BR-8077 TCGA-BR-8078 
        0.16         1.08         0.82         1.32         0.69         0.95 
TCGA-BR-8080 TCGA-BR-8081 TCGA-BR-8284 TCGA-BR-8285 TCGA-BR-8286 TCGA-BR-8291 
        0.49         0.46         0.72         0.26         0.43         1.18 
TCGA-BR-8296 TCGA-BR-8297 TCGA-BR-8592 TCGA-BR-A4IU TCGA-BR-A4IV TCGA-BR-A4IY 
        1.48         0.76         0.20         0.59         0.92         0.39 
TCGA-BR-A4IZ TCGA-BR-A4J1 TCGA-BR-A4J2 TCGA-BR-A4J5 TCGA-BR-A4J6 TCGA-BR-A4J8 
        0.79         0.72         0.79         0.43         0.13         0.23 
TCGA-BR-A4PF TCGA-BR-A4QI TCGA-BR-A4QL TCGA-CD-5798 TCGA-CD-5799 TCGA-CD-5800 
        0.72         0.49         2.24         0.82         0.69         0.36 
TCGA-CD-5801 TCGA-CD-5802 TCGA-CD-5803 TCGA-CG-4300 TCGA-CG-4301 TCGA-CG-4304 
        0.49         0.30         0.07        20.02         3.02        27.02 
TCGA-CG-4305 TCGA-CG-4306 TCGA-CG-4437 TCGA-CG-4438 TCGA-CG-4440 TCGA-CG-4441 
       15.95         1.02         8.05        54.05         4.01        14.01 
TCGA-CG-4443 TCGA-CG-4444 TCGA-CG-4449 TCGA-CG-4455 TCGA-CG-4460 TCGA-CG-4462 
       29.98        47.05        19.07        12.03        21.99         1.02 
TCGA-CG-4465 TCGA-CG-4466 TCGA-CG-4469 TCGA-CG-4472 TCGA-CG-4474 TCGA-CG-4477 
        8.98        18.94         7.07        12.00         1.02         1.02 
TCGA-CG-5716 TCGA-CG-5717 TCGA-CG-5718 TCGA-CG-5719 TCGA-CG-5720 TCGA-CG-5721 
        1.02         6.94         1.02         1.02         0.99         5.98 
TCGA-CG-5722 TCGA-CG-5723 TCGA-CG-5724 TCGA-CG-5725 TCGA-CG-5726 TCGA-CG-5727 
        0.95        70.06        12.03        15.02        28.96        31.04 
TCGA-CG-5728 TCGA-CG-5730 TCGA-CG-5732 TCGA-CG-5733 TCGA-CG-5734 TCGA-D7-5577 
       65.10         4.01        55.04        21.07         7.99         8.65 
TCGA-D7-5578 TCGA-D7-5579 TCGA-D7-6518 TCGA-D7-6519 TCGA-D7-6520 TCGA-D7-6521 
        3.58         4.54         9.80        15.65         9.63         8.19 
TCGA-D7-6522 TCGA-D7-6524 TCGA-D7-6525 TCGA-D7-6526 TCGA-D7-6527 TCGA-D7-6815 
        6.90         0.69         5.95         6.61         4.14         3.65 
TCGA-D7-6817 TCGA-D7-6820 TCGA-EQ-8122 TCGA-F1-6177 TCGA-F1-6874 TCGA-F1-6875 
        4.70         2.93         7.79         6.54         2.01        72.23 
TCGA-FP-7735 TCGA-FP-7829 TCGA-FP-7916 TCGA-FP-7998 TCGA-FP-8099 TCGA-FP-8209 
        0.39         0.20         3.02         3.58         1.02        59.05 
TCGA-FP-8210 TCGA-FP-8631 TCGA-HJ-7597 TCGA-IN-7806 TCGA-IN-7808 TCGA-IP-7968 
        5.03         0.56        26.43         6.87         3.55         2.53 

      9P GAIN CNV 9P GAIN WILD-TYPE 
             0.10              0.07 
      9P GAIN CNV 9P GAIN WILD-TYPE 
            52.96             72.23 
      9P GAIN CNV 9P GAIN WILD-TYPE 
            0.990             1.285 
[1] "0.1 - 53.0 (1.0)" "0.1 - 72.2 (1.3)"
       TCGA-B7-5816        TCGA-B7-5818        TCGA-BR-6452        TCGA-BR-6455 
"9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" 
       TCGA-BR-6457        TCGA-BR-6458        TCGA-BR-6563        TCGA-BR-6564 
"9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" 
       TCGA-BR-6565        TCGA-BR-6566        TCGA-BR-6705        TCGA-BR-6706 
"9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" 
       TCGA-BR-6707        TCGA-BR-6709        TCGA-BR-6710        TCGA-BR-6801 
      "9P GAIN CNV" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" 
       TCGA-BR-6802        TCGA-BR-6803        TCGA-BR-6852        TCGA-BR-7196 
"9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" 
       TCGA-BR-7197        TCGA-BR-7703        TCGA-BR-7704        TCGA-BR-7707 
"9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE"       "9P GAIN CNV" 
       TCGA-BR-7715        TCGA-BR-7716        TCGA-BR-7717        TCGA-BR-7722 
"9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" 
       TCGA-BR-7723        TCGA-BR-7851        TCGA-BR-7901        TCGA-BR-7957 
"9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" 
       TCGA-BR-7958        TCGA-BR-7959        TCGA-BR-8059        TCGA-BR-8060 
"9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" 
       TCGA-BR-8077        TCGA-BR-8078        TCGA-BR-8080        TCGA-BR-8081 
"9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" 
       TCGA-BR-8284        TCGA-BR-8285        TCGA-BR-8286        TCGA-BR-8289 
"9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE"       "9P GAIN CNV" 
       TCGA-BR-8291        TCGA-BR-8295        TCGA-BR-8296        TCGA-BR-8297 
"9P GAIN WILD-TYPE"       "9P GAIN CNV" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" 
       TCGA-BR-8592        TCGA-BR-A4IU        TCGA-BR-A4IV        TCGA-BR-A4IY 
"9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" 
       TCGA-BR-A4IZ        TCGA-BR-A4J1        TCGA-BR-A4J2        TCGA-BR-A4J4 
"9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE"       "9P GAIN CNV" 
       TCGA-BR-A4J5        TCGA-BR-A4J6        TCGA-BR-A4J8        TCGA-BR-A4J9 
"9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE"       "9P GAIN CNV" 
       TCGA-BR-A4PF        TCGA-BR-A4QI        TCGA-BR-A4QL        TCGA-CD-5798 
"9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" 
       TCGA-CD-5799        TCGA-CD-5800        TCGA-CD-5801        TCGA-CD-5802 
"9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" 
       TCGA-CD-5803        TCGA-CG-4300        TCGA-CG-4301        TCGA-CG-4304 
"9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" 
       TCGA-CG-4305        TCGA-CG-4306        TCGA-CG-4436        TCGA-CG-4437 
"9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE"       "9P GAIN CNV" "9P GAIN WILD-TYPE" 
       TCGA-CG-4438        TCGA-CG-4440        TCGA-CG-4441        TCGA-CG-4443 
"9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" 
       TCGA-CG-4444        TCGA-CG-4449        TCGA-CG-4455        TCGA-CG-4460 
"9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" 
       TCGA-CG-4462        TCGA-CG-4465        TCGA-CG-4466        TCGA-CG-4469 
"9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" 
       TCGA-CG-4472        TCGA-CG-4474        TCGA-CG-4477        TCGA-CG-5716 
"9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" 
       TCGA-CG-5717        TCGA-CG-5718        TCGA-CG-5719        TCGA-CG-5720 
"9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" 
       TCGA-CG-5721        TCGA-CG-5722        TCGA-CG-5723        TCGA-CG-5724 
"9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" 
       TCGA-CG-5725        TCGA-CG-5726        TCGA-CG-5727        TCGA-CG-5728 
"9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" 
       TCGA-CG-5730        TCGA-CG-5732        TCGA-CG-5733        TCGA-CG-5734 
"9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" 
       TCGA-D7-5577        TCGA-D7-5578        TCGA-D7-5579        TCGA-D7-6518 
"9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" 
       TCGA-D7-6519        TCGA-D7-6520        TCGA-D7-6521        TCGA-D7-6522 
"9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" 
       TCGA-D7-6524        TCGA-D7-6525        TCGA-D7-6526        TCGA-D7-6527 
"9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" 
       TCGA-D7-6528        TCGA-D7-6815        TCGA-D7-6817        TCGA-D7-6818 
      "9P GAIN CNV" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE"       "9P GAIN CNV" 
       TCGA-D7-6820        TCGA-D7-6822        TCGA-EQ-5647        TCGA-EQ-8122 
"9P GAIN WILD-TYPE"       "9P GAIN CNV"       "9P GAIN CNV" "9P GAIN WILD-TYPE" 
       TCGA-F1-6177        TCGA-F1-6874        TCGA-F1-6875        TCGA-FP-7735 
"9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" 
       TCGA-FP-7829        TCGA-FP-7916        TCGA-FP-7998        TCGA-FP-8099 
"9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" 
       TCGA-FP-8209        TCGA-FP-8210        TCGA-FP-8631        TCGA-HJ-7597 
"9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" 
       TCGA-IN-7806        TCGA-IN-7808        TCGA-IP-7968 
"9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" 
       TCGA-B7-5816        TCGA-B7-5818        TCGA-BR-6452        TCGA-BR-6455 
"9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" 
       TCGA-BR-6457        TCGA-BR-6458        TCGA-BR-6563        TCGA-BR-6564 
"9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" 
       TCGA-BR-6565        TCGA-BR-6566        TCGA-BR-6705        TCGA-BR-6706 
"9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" 
       TCGA-BR-6707        TCGA-BR-6709        TCGA-BR-6710        TCGA-BR-6801 
      "9P GAIN CNV" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" 
       TCGA-BR-6802        TCGA-BR-6803        TCGA-BR-6852        TCGA-BR-7196 
"9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" 
       TCGA-BR-7197        TCGA-BR-7703        TCGA-BR-7704        TCGA-BR-7707 
"9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE"       "9P GAIN CNV" 
       TCGA-BR-7715        TCGA-BR-7716        TCGA-BR-7717        TCGA-BR-7722 
"9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" 
       TCGA-BR-7723        TCGA-BR-7851        TCGA-BR-7901        TCGA-BR-7957 
"9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" 
       TCGA-BR-7958        TCGA-BR-7959        TCGA-BR-8059        TCGA-BR-8060 
"9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" 
       TCGA-BR-8077        TCGA-BR-8078        TCGA-BR-8080        TCGA-BR-8081 
"9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" 
       TCGA-BR-8284        TCGA-BR-8285        TCGA-BR-8286        TCGA-BR-8289 
"9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE"       "9P GAIN CNV" 
       TCGA-BR-8291        TCGA-BR-8295        TCGA-BR-8296        TCGA-BR-8297 
"9P GAIN WILD-TYPE"       "9P GAIN CNV" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" 
       TCGA-BR-8592        TCGA-BR-A4IU        TCGA-BR-A4IV        TCGA-BR-A4IY 
"9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" 
       TCGA-BR-A4IZ        TCGA-BR-A4J1        TCGA-BR-A4J2        TCGA-BR-A4J4 
"9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE"       "9P GAIN CNV" 
       TCGA-BR-A4J5        TCGA-BR-A4J6        TCGA-BR-A4J8        TCGA-BR-A4J9 
"9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE"       "9P GAIN CNV" 
       TCGA-BR-A4PF        TCGA-BR-A4QI        TCGA-BR-A4QL        TCGA-CD-5798 
"9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" 
       TCGA-CD-5799        TCGA-CD-5800        TCGA-CD-5801        TCGA-CD-5802 
"9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" 
       TCGA-CD-5803        TCGA-CG-4300        TCGA-CG-4301        TCGA-CG-4304 
"9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" 
       TCGA-CG-4305        TCGA-CG-4306        TCGA-CG-4436        TCGA-CG-4437 
"9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE"       "9P GAIN CNV" "9P GAIN WILD-TYPE" 
       TCGA-CG-4438        TCGA-CG-4440        TCGA-CG-4441        TCGA-CG-4443 
"9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" 
       TCGA-CG-4444        TCGA-CG-4449        TCGA-CG-4455        TCGA-CG-4460 
"9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" 
       TCGA-CG-4462        TCGA-CG-4465        TCGA-CG-4466        TCGA-CG-4469 
"9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" 
       TCGA-CG-4472        TCGA-CG-4474        TCGA-CG-4477        TCGA-CG-5716 
"9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" 
       TCGA-CG-5717        TCGA-CG-5718        TCGA-CG-5719        TCGA-CG-5720 
"9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" 
       TCGA-CG-5721        TCGA-CG-5722        TCGA-CG-5723        TCGA-CG-5724 
"9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" 
       TCGA-CG-5725        TCGA-CG-5726        TCGA-CG-5727        TCGA-CG-5728 
"9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" 
       TCGA-CG-5730        TCGA-CG-5732        TCGA-CG-5733        TCGA-CG-5734 
"9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" 
       TCGA-D7-5577        TCGA-D7-5578        TCGA-D7-5579        TCGA-D7-6518 
"9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" 
       TCGA-D7-6519        TCGA-D7-6520        TCGA-D7-6521        TCGA-D7-6522 
"9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" 
       TCGA-D7-6524        TCGA-D7-6525        TCGA-D7-6526        TCGA-D7-6527 
"9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" 
       TCGA-D7-6528        TCGA-D7-6815        TCGA-D7-6817        TCGA-D7-6818 
      "9P GAIN CNV" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE"       "9P GAIN CNV" 
       TCGA-D7-6820        TCGA-D7-6822        TCGA-EQ-5647        TCGA-EQ-8122 
"9P GAIN WILD-TYPE"       "9P GAIN CNV"       "9P GAIN CNV" "9P GAIN WILD-TYPE" 
       TCGA-F1-6177        TCGA-F1-6874        TCGA-F1-6875        TCGA-FP-7735 
"9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" 
       TCGA-FP-7829        TCGA-FP-7916        TCGA-FP-7998        TCGA-FP-8099 
"9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" 
       TCGA-FP-8209        TCGA-FP-8210        TCGA-FP-8631        TCGA-HJ-7597 
"9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" 
       TCGA-IN-7806        TCGA-IN-7808        TCGA-IP-7968 
"9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" 
       TCGA-B7-5816        TCGA-B7-5818        TCGA-BR-6452        TCGA-BR-6455 
"9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" 
       TCGA-BR-6457        TCGA-BR-6458        TCGA-BR-6563        TCGA-BR-6564 
"9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" 
       TCGA-BR-6565        TCGA-BR-6566        TCGA-BR-6705        TCGA-BR-6706 
"9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" 
       TCGA-BR-6707        TCGA-BR-6709        TCGA-BR-6710        TCGA-BR-6801 
      "9P GAIN CNV" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" 
       TCGA-BR-6802        TCGA-BR-6803        TCGA-BR-6852        TCGA-BR-7196 
"9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" 
       TCGA-BR-7197        TCGA-BR-7703        TCGA-BR-7704        TCGA-BR-7707 
"9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE"       "9P GAIN CNV" 
       TCGA-BR-7715        TCGA-BR-7716        TCGA-BR-7717        TCGA-BR-7722 
"9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" 
       TCGA-BR-7723        TCGA-BR-7851        TCGA-BR-7901        TCGA-BR-7957 
"9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" 
       TCGA-BR-7958        TCGA-BR-7959        TCGA-BR-8059        TCGA-BR-8060 
"9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" 
       TCGA-BR-8077        TCGA-BR-8078        TCGA-BR-8080        TCGA-BR-8081 
"9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" 
       TCGA-BR-8284        TCGA-BR-8285        TCGA-BR-8286        TCGA-BR-8289 
"9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE"       "9P GAIN CNV" 
       TCGA-BR-8291        TCGA-BR-8295        TCGA-BR-8296        TCGA-BR-8297 
"9P GAIN WILD-TYPE"       "9P GAIN CNV" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" 
       TCGA-BR-8592        TCGA-BR-A4IU        TCGA-BR-A4IV        TCGA-BR-A4IY 
"9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" 
       TCGA-BR-A4IZ        TCGA-BR-A4J1        TCGA-BR-A4J2        TCGA-BR-A4J4 
"9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE"       "9P GAIN CNV" 
       TCGA-BR-A4J5        TCGA-BR-A4J6        TCGA-BR-A4J8        TCGA-BR-A4J9 
"9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE"       "9P GAIN CNV" 
       TCGA-BR-A4PF        TCGA-BR-A4QI        TCGA-BR-A4QL        TCGA-CD-5798 
"9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" 
       TCGA-CD-5799        TCGA-CD-5800        TCGA-CD-5801        TCGA-CD-5802 
"9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" 
       TCGA-CD-5803        TCGA-CG-4300        TCGA-CG-4301        TCGA-CG-4304 
"9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" 
       TCGA-CG-4305        TCGA-CG-4306        TCGA-CG-4436        TCGA-CG-4437 
"9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE"       "9P GAIN CNV" "9P GAIN WILD-TYPE" 
       TCGA-CG-4438        TCGA-CG-4440        TCGA-CG-4441        TCGA-CG-4443 
"9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" 
       TCGA-CG-4444        TCGA-CG-4449        TCGA-CG-4455        TCGA-CG-4460 
"9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" 
       TCGA-CG-4462        TCGA-CG-4465        TCGA-CG-4466        TCGA-CG-4469 
"9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" 
       TCGA-CG-4472        TCGA-CG-4474        TCGA-CG-4477        TCGA-CG-5716 
"9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" 
       TCGA-CG-5717        TCGA-CG-5718        TCGA-CG-5719        TCGA-CG-5720 
"9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" 
       TCGA-CG-5721        TCGA-CG-5722        TCGA-CG-5723        TCGA-CG-5724 
"9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" 
       TCGA-CG-5725        TCGA-CG-5726        TCGA-CG-5727        TCGA-CG-5728 
"9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" 
       TCGA-CG-5730        TCGA-CG-5732        TCGA-CG-5733        TCGA-CG-5734 
"9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" 
       TCGA-D7-5577        TCGA-D7-5578        TCGA-D7-5579        TCGA-D7-6518 
"9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" 
       TCGA-D7-6519        TCGA-D7-6520        TCGA-D7-6521        TCGA-D7-6522 
"9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" 
       TCGA-D7-6524        TCGA-D7-6525        TCGA-D7-6526        TCGA-D7-6527 
"9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" 
       TCGA-D7-6528        TCGA-D7-6815        TCGA-D7-6817        TCGA-D7-6818 
      "9P GAIN CNV" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE"       "9P GAIN CNV" 
       TCGA-D7-6820        TCGA-D7-6822        TCGA-EQ-5647        TCGA-EQ-8122 
"9P GAIN WILD-TYPE"       "9P GAIN CNV"       "9P GAIN CNV" "9P GAIN WILD-TYPE" 
       TCGA-F1-6177        TCGA-F1-6874        TCGA-F1-6875        TCGA-FP-7735 
"9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" 
       TCGA-FP-7829        TCGA-FP-7916        TCGA-FP-7998        TCGA-FP-8099 
"9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" 
       TCGA-FP-8209        TCGA-FP-8210        TCGA-FP-8631        TCGA-HJ-7597 
"9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" 
       TCGA-IN-7806        TCGA-IN-7808        TCGA-IP-7968 
"9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" 
[1] "hr=" "1.1"
D16V2, continuous
D16V3, binary
[1] "tbl2"
                   cls
clus                [,1] [,2]
  9P GAIN CNV          7    8
  9P GAIN WILD-TYPE   65  100
        clus
vv       9P GAIN CNV 9P GAIN WILD-TYPE
  FEMALE           7                65
  MALE             8               100
                   vv
clus                STOMACH  ADENOCARCINOMA  DIFFUSE TYPE
  9P GAIN CNV                                           0
  9P GAIN WILD-TYPE                                    10
                   vv
clus                STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  9P GAIN CNV                                                            3
  9P GAIN WILD-TYPE                                                     13
                   vv
clus                STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  9P GAIN CNV                                                                       1
  9P GAIN WILD-TYPE                                                                 7
                   vv
clus                STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE
  9P GAIN CNV                                                              0
  9P GAIN WILD-TYPE                                                        3
                   vv
clus                STOMACH ADENOCARCINOMA  SIGNET RING TYPE
  9P GAIN CNV                                              0
  9P GAIN WILD-TYPE                                        1
                   vv
clus                STOMACH ADENOCARCINOMA - DIFFUSE TYPE
  9P GAIN CNV                                           1
  9P GAIN WILD-TYPE                                    15
                   vv
clus                STOMACH ADENOCARCINOMA - NOT OTHERWISE SPECIFIED (NOS)
  9P GAIN CNV                                                            6
  9P GAIN WILD-TYPE                                                     67
                   vv
clus                STOMACH INTESTINAL ADENOCARCINOMA - MUCINOUS TYPE
  9P GAIN CNV                                                       0
  9P GAIN WILD-TYPE                                                 7
                   vv
clus                STOMACH INTESTINAL ADENOCARCINOMA - PAPILLARY TYPE
  9P GAIN CNV                                                        0
  9P GAIN WILD-TYPE                                                  3
                   vv
clus                STOMACH INTESTINAL ADENOCARCINOMA - TUBULAR TYPE
  9P GAIN CNV                                                      2
  9P GAIN WILD-TYPE                                                8
                   vv
clus                STOMACH INTESTINAL ADENOCARCINOMA - TYPE NOT OTHERWISE SPECIFIED (NOS)
  9P GAIN CNV                                                                            2
  9P GAIN WILD-TYPE                                                                     26
D16V4, multiclass
                   vv
clus                T1 T2 T3 T4
  9P GAIN CNV        2  5  2  1
  9P GAIN WILD-TYPE  4 47 54 17
D16V5, multiclass
    clus
vv   9P GAIN CNV 9P GAIN WILD-TYPE
  T1           2                 4
  T2           5                47
  T3           2                54
  T4           1                17
                   vv
clus                N0 N1 N2 N3
  9P GAIN CNV        6  2  0  2
  9P GAIN WILD-TYPE 38 47 23 13
D16V6, multiclass
    clus
vv   9P GAIN CNV 9P GAIN WILD-TYPE
  N0           6                38
  N1           2                47
  N2           0                23
  N3           2                13
                   vv
clus                 M0  M1  MX
  9P GAIN CNV        10   1   0
  9P GAIN WILD-TYPE 108  15   8
D16V7, multiclass
    clus
vv   9P GAIN CNV 9P GAIN WILD-TYPE
  M0          10               108
  M1           1                15
  MX           0                 8
                   vv
clus                 I II III IV
  9P GAIN CNV        5  2   0  2
  9P GAIN WILD-TYPE 19 35  39 24
D16V8, multiclass
     clus
vv    9P GAIN CNV 9P GAIN WILD-TYPE
  I             5                19
  II            2                35
  III           0                39
  IV            2                24
D16V9, binary
[1] "tbl2"
                   cls
clus                [,1] [,2]
  9P GAIN CNV          1   14
  9P GAIN WILD-TYPE    4  161
     clus
vv    9P GAIN CNV 9P GAIN WILD-TYPE
  NO            1                 4
  YES          14               161
                   vv
clus                 R0  R1  R2  RX
  9P GAIN CNV        12   0   1   2
  9P GAIN WILD-TYPE 113   7  11  23
D16V10, multiclass
    clus
vv   9P GAIN CNV 9P GAIN WILD-TYPE
  R0          12               113
  R1           0                 7
  R2           1                11
  RX           2                23
D16V11, continuous

Clustering(17) Variable = 9q gain
D17V1, survival
                   sevent
clus2                 0   1
  9Q GAIN CNV        13   1
  9Q GAIN WILD-TYPE 111  18
      9Q GAIN CNV 9Q GAIN WILD-TYPE 
               14               129 
      9Q GAIN CNV 9Q GAIN WILD-TYPE 
                1                18 
$`9Q GAIN CNV`
TCGA-BR-6707 TCGA-BR-7704 TCGA-BR-7707 TCGA-BR-7959 TCGA-BR-8289 TCGA-BR-8295 
        0.99         1.25         0.13         1.08         0.26         1.55 
TCGA-BR-A4J4 TCGA-BR-A4J9 TCGA-CG-4436 TCGA-D7-6528 TCGA-D7-6818 TCGA-EQ-5647 
        0.53         0.10        52.96         1.68         4.04         0.62 
TCGA-FP-7735 TCGA-IN-7808 
        0.39         3.55 

$`9Q GAIN WILD-TYPE`
TCGA-B7-5816 TCGA-B7-5818 TCGA-BR-6452 TCGA-BR-6455 TCGA-BR-6457 TCGA-BR-6458 
        5.62         0.10         0.95         1.41         1.35         1.35 
TCGA-BR-6563 TCGA-BR-6564 TCGA-BR-6565 TCGA-BR-6566 TCGA-BR-6705 TCGA-BR-6706 
        0.85         0.82         0.62         0.62         1.71         2.17 
TCGA-BR-6709 TCGA-BR-6710 TCGA-BR-6801 TCGA-BR-6802 TCGA-BR-6803 TCGA-BR-6852 
        1.22         0.66         1.12         0.76         0.66         0.26 
TCGA-BR-7196 TCGA-BR-7197 TCGA-BR-7703 TCGA-BR-7715 TCGA-BR-7716 TCGA-BR-7717 
        1.22         1.48         0.46         1.05         0.82         0.69 
TCGA-BR-7722 TCGA-BR-7723 TCGA-BR-7851 TCGA-BR-7901 TCGA-BR-7957 TCGA-BR-7958 
        0.16         4.54         0.99         0.95         0.69         0.16 
TCGA-BR-8059 TCGA-BR-8060 TCGA-BR-8077 TCGA-BR-8078 TCGA-BR-8080 TCGA-BR-8081 
        0.82         1.32         0.69         0.95         0.49         0.46 
TCGA-BR-8284 TCGA-BR-8285 TCGA-BR-8286 TCGA-BR-8291 TCGA-BR-8296 TCGA-BR-8297 
        0.72         0.26         0.43         1.18         1.48         0.76 
TCGA-BR-8592 TCGA-BR-A4IU TCGA-BR-A4IV TCGA-BR-A4IY TCGA-BR-A4IZ TCGA-BR-A4J1 
        0.20         0.59         0.92         0.39         0.79         0.72 
TCGA-BR-A4J2 TCGA-BR-A4J5 TCGA-BR-A4J6 TCGA-BR-A4J8 TCGA-BR-A4PF TCGA-BR-A4QI 
        0.79         0.43         0.13         0.23         0.72         0.49 
TCGA-BR-A4QL TCGA-CD-5798 TCGA-CD-5799 TCGA-CD-5800 TCGA-CD-5801 TCGA-CD-5802 
        2.24         0.82         0.69         0.36         0.49         0.30 
TCGA-CD-5803 TCGA-CG-4300 TCGA-CG-4301 TCGA-CG-4304 TCGA-CG-4305 TCGA-CG-4306 
        0.07        20.02         3.02        27.02        15.95         1.02 
TCGA-CG-4437 TCGA-CG-4438 TCGA-CG-4440 TCGA-CG-4441 TCGA-CG-4443 TCGA-CG-4444 
        8.05        54.05         4.01        14.01        29.98        47.05 
TCGA-CG-4449 TCGA-CG-4455 TCGA-CG-4460 TCGA-CG-4462 TCGA-CG-4465 TCGA-CG-4466 
       19.07        12.03        21.99         1.02         8.98        18.94 
TCGA-CG-4469 TCGA-CG-4472 TCGA-CG-4474 TCGA-CG-4477 TCGA-CG-5716 TCGA-CG-5717 
        7.07        12.00         1.02         1.02         1.02         6.94 
TCGA-CG-5718 TCGA-CG-5719 TCGA-CG-5720 TCGA-CG-5721 TCGA-CG-5722 TCGA-CG-5723 
        1.02         1.02         0.99         5.98         0.95        70.06 
TCGA-CG-5724 TCGA-CG-5725 TCGA-CG-5726 TCGA-CG-5727 TCGA-CG-5728 TCGA-CG-5730 
       12.03        15.02        28.96        31.04        65.10         4.01 
TCGA-CG-5732 TCGA-CG-5733 TCGA-CG-5734 TCGA-D7-5577 TCGA-D7-5578 TCGA-D7-5579 
       55.04        21.07         7.99         8.65         3.58         4.54 
TCGA-D7-6518 TCGA-D7-6519 TCGA-D7-6520 TCGA-D7-6521 TCGA-D7-6522 TCGA-D7-6524 
        9.80        15.65         9.63         8.19         6.90         0.69 
TCGA-D7-6525 TCGA-D7-6526 TCGA-D7-6527 TCGA-D7-6815 TCGA-D7-6817 TCGA-D7-6820 
        5.95         6.61         4.14         3.65         4.70         2.93 
TCGA-D7-6822 TCGA-EQ-8122 TCGA-F1-6177 TCGA-F1-6874 TCGA-F1-6875 TCGA-FP-7829 
        4.27         7.79         6.54         2.01        72.23         0.20 
TCGA-FP-7916 TCGA-FP-7998 TCGA-FP-8099 TCGA-FP-8209 TCGA-FP-8210 TCGA-FP-8631 
        3.02         3.58         1.02        59.05         5.03         0.56 
TCGA-HJ-7597 TCGA-IN-7806 TCGA-IP-7968 
       26.43         6.87         2.53 

      9Q GAIN CNV 9Q GAIN WILD-TYPE 
             0.10              0.07 
      9Q GAIN CNV 9Q GAIN WILD-TYPE 
            52.96             72.23 
      9Q GAIN CNV 9Q GAIN WILD-TYPE 
            1.035             1.350 
[1] "0.1 - 53.0 (1.0)" "0.1 - 72.2 (1.4)"
       TCGA-B7-5816        TCGA-B7-5818        TCGA-BR-6452        TCGA-BR-6455 
"9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" 
       TCGA-BR-6457        TCGA-BR-6458        TCGA-BR-6563        TCGA-BR-6564 
"9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" 
       TCGA-BR-6565        TCGA-BR-6566        TCGA-BR-6705        TCGA-BR-6706 
"9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" 
       TCGA-BR-6707        TCGA-BR-6709        TCGA-BR-6710        TCGA-BR-6801 
      "9Q GAIN CNV" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" 
       TCGA-BR-6802        TCGA-BR-6803        TCGA-BR-6852        TCGA-BR-7196 
"9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" 
       TCGA-BR-7197        TCGA-BR-7703        TCGA-BR-7704        TCGA-BR-7707 
"9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE"       "9Q GAIN CNV"       "9Q GAIN CNV" 
       TCGA-BR-7715        TCGA-BR-7716        TCGA-BR-7717        TCGA-BR-7722 
"9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" 
       TCGA-BR-7723        TCGA-BR-7851        TCGA-BR-7901        TCGA-BR-7957 
"9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" 
       TCGA-BR-7958        TCGA-BR-7959        TCGA-BR-8059        TCGA-BR-8060 
"9Q GAIN WILD-TYPE"       "9Q GAIN CNV" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" 
       TCGA-BR-8077        TCGA-BR-8078        TCGA-BR-8080        TCGA-BR-8081 
"9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" 
       TCGA-BR-8284        TCGA-BR-8285        TCGA-BR-8286        TCGA-BR-8289 
"9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE"       "9Q GAIN CNV" 
       TCGA-BR-8291        TCGA-BR-8295        TCGA-BR-8296        TCGA-BR-8297 
"9Q GAIN WILD-TYPE"       "9Q GAIN CNV" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" 
       TCGA-BR-8592        TCGA-BR-A4IU        TCGA-BR-A4IV        TCGA-BR-A4IY 
"9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" 
       TCGA-BR-A4IZ        TCGA-BR-A4J1        TCGA-BR-A4J2        TCGA-BR-A4J4 
"9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE"       "9Q GAIN CNV" 
       TCGA-BR-A4J5        TCGA-BR-A4J6        TCGA-BR-A4J8        TCGA-BR-A4J9 
"9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE"       "9Q GAIN CNV" 
       TCGA-BR-A4PF        TCGA-BR-A4QI        TCGA-BR-A4QL        TCGA-CD-5798 
"9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" 
       TCGA-CD-5799        TCGA-CD-5800        TCGA-CD-5801        TCGA-CD-5802 
"9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" 
       TCGA-CD-5803        TCGA-CG-4300        TCGA-CG-4301        TCGA-CG-4304 
"9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" 
       TCGA-CG-4305        TCGA-CG-4306        TCGA-CG-4436        TCGA-CG-4437 
"9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE"       "9Q GAIN CNV" "9Q GAIN WILD-TYPE" 
       TCGA-CG-4438        TCGA-CG-4440        TCGA-CG-4441        TCGA-CG-4443 
"9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" 
       TCGA-CG-4444        TCGA-CG-4449        TCGA-CG-4455        TCGA-CG-4460 
"9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" 
       TCGA-CG-4462        TCGA-CG-4465        TCGA-CG-4466        TCGA-CG-4469 
"9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" 
       TCGA-CG-4472        TCGA-CG-4474        TCGA-CG-4477        TCGA-CG-5716 
"9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" 
       TCGA-CG-5717        TCGA-CG-5718        TCGA-CG-5719        TCGA-CG-5720 
"9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" 
       TCGA-CG-5721        TCGA-CG-5722        TCGA-CG-5723        TCGA-CG-5724 
"9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" 
       TCGA-CG-5725        TCGA-CG-5726        TCGA-CG-5727        TCGA-CG-5728 
"9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" 
       TCGA-CG-5730        TCGA-CG-5732        TCGA-CG-5733        TCGA-CG-5734 
"9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" 
       TCGA-D7-5577        TCGA-D7-5578        TCGA-D7-5579        TCGA-D7-6518 
"9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" 
       TCGA-D7-6519        TCGA-D7-6520        TCGA-D7-6521        TCGA-D7-6522 
"9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" 
       TCGA-D7-6524        TCGA-D7-6525        TCGA-D7-6526        TCGA-D7-6527 
"9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" 
       TCGA-D7-6528        TCGA-D7-6815        TCGA-D7-6817        TCGA-D7-6818 
      "9Q GAIN CNV" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE"       "9Q GAIN CNV" 
       TCGA-D7-6820        TCGA-D7-6822        TCGA-EQ-5647        TCGA-EQ-8122 
"9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE"       "9Q GAIN CNV" "9Q GAIN WILD-TYPE" 
       TCGA-F1-6177        TCGA-F1-6874        TCGA-F1-6875        TCGA-FP-7735 
"9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE"       "9Q GAIN CNV" 
       TCGA-FP-7829        TCGA-FP-7916        TCGA-FP-7998        TCGA-FP-8099 
"9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" 
       TCGA-FP-8209        TCGA-FP-8210        TCGA-FP-8631        TCGA-HJ-7597 
"9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" 
       TCGA-IN-7806        TCGA-IN-7808        TCGA-IP-7968 
"9Q GAIN WILD-TYPE"       "9Q GAIN CNV" "9Q GAIN WILD-TYPE" 
       TCGA-B7-5816        TCGA-B7-5818        TCGA-BR-6452        TCGA-BR-6455 
"9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" 
       TCGA-BR-6457        TCGA-BR-6458        TCGA-BR-6563        TCGA-BR-6564 
"9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" 
       TCGA-BR-6565        TCGA-BR-6566        TCGA-BR-6705        TCGA-BR-6706 
"9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" 
       TCGA-BR-6707        TCGA-BR-6709        TCGA-BR-6710        TCGA-BR-6801 
      "9Q GAIN CNV" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" 
       TCGA-BR-6802        TCGA-BR-6803        TCGA-BR-6852        TCGA-BR-7196 
"9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" 
       TCGA-BR-7197        TCGA-BR-7703        TCGA-BR-7704        TCGA-BR-7707 
"9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE"       "9Q GAIN CNV"       "9Q GAIN CNV" 
       TCGA-BR-7715        TCGA-BR-7716        TCGA-BR-7717        TCGA-BR-7722 
"9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" 
       TCGA-BR-7723        TCGA-BR-7851        TCGA-BR-7901        TCGA-BR-7957 
"9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" 
       TCGA-BR-7958        TCGA-BR-7959        TCGA-BR-8059        TCGA-BR-8060 
"9Q GAIN WILD-TYPE"       "9Q GAIN CNV" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" 
       TCGA-BR-8077        TCGA-BR-8078        TCGA-BR-8080        TCGA-BR-8081 
"9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" 
       TCGA-BR-8284        TCGA-BR-8285        TCGA-BR-8286        TCGA-BR-8289 
"9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE"       "9Q GAIN CNV" 
       TCGA-BR-8291        TCGA-BR-8295        TCGA-BR-8296        TCGA-BR-8297 
"9Q GAIN WILD-TYPE"       "9Q GAIN CNV" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" 
       TCGA-BR-8592        TCGA-BR-A4IU        TCGA-BR-A4IV        TCGA-BR-A4IY 
"9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" 
       TCGA-BR-A4IZ        TCGA-BR-A4J1        TCGA-BR-A4J2        TCGA-BR-A4J4 
"9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE"       "9Q GAIN CNV" 
       TCGA-BR-A4J5        TCGA-BR-A4J6        TCGA-BR-A4J8        TCGA-BR-A4J9 
"9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE"       "9Q GAIN CNV" 
       TCGA-BR-A4PF        TCGA-BR-A4QI        TCGA-BR-A4QL        TCGA-CD-5798 
"9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" 
       TCGA-CD-5799        TCGA-CD-5800        TCGA-CD-5801        TCGA-CD-5802 
"9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" 
       TCGA-CD-5803        TCGA-CG-4300        TCGA-CG-4301        TCGA-CG-4304 
"9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" 
       TCGA-CG-4305        TCGA-CG-4306        TCGA-CG-4436        TCGA-CG-4437 
"9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE"       "9Q GAIN CNV" "9Q GAIN WILD-TYPE" 
       TCGA-CG-4438        TCGA-CG-4440        TCGA-CG-4441        TCGA-CG-4443 
"9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" 
       TCGA-CG-4444        TCGA-CG-4449        TCGA-CG-4455        TCGA-CG-4460 
"9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" 
       TCGA-CG-4462        TCGA-CG-4465        TCGA-CG-4466        TCGA-CG-4469 
"9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" 
       TCGA-CG-4472        TCGA-CG-4474        TCGA-CG-4477        TCGA-CG-5716 
"9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" 
       TCGA-CG-5717        TCGA-CG-5718        TCGA-CG-5719        TCGA-CG-5720 
"9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" 
       TCGA-CG-5721        TCGA-CG-5722        TCGA-CG-5723        TCGA-CG-5724 
"9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" 
       TCGA-CG-5725        TCGA-CG-5726        TCGA-CG-5727        TCGA-CG-5728 
"9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" 
       TCGA-CG-5730        TCGA-CG-5732        TCGA-CG-5733        TCGA-CG-5734 
"9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" 
       TCGA-D7-5577        TCGA-D7-5578        TCGA-D7-5579        TCGA-D7-6518 
"9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" 
       TCGA-D7-6519        TCGA-D7-6520        TCGA-D7-6521        TCGA-D7-6522 
"9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" 
       TCGA-D7-6524        TCGA-D7-6525        TCGA-D7-6526        TCGA-D7-6527 
"9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" 
       TCGA-D7-6528        TCGA-D7-6815        TCGA-D7-6817        TCGA-D7-6818 
      "9Q GAIN CNV" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE"       "9Q GAIN CNV" 
       TCGA-D7-6820        TCGA-D7-6822        TCGA-EQ-5647        TCGA-EQ-8122 
"9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE"       "9Q GAIN CNV" "9Q GAIN WILD-TYPE" 
       TCGA-F1-6177        TCGA-F1-6874        TCGA-F1-6875        TCGA-FP-7735 
"9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE"       "9Q GAIN CNV" 
       TCGA-FP-7829        TCGA-FP-7916        TCGA-FP-7998        TCGA-FP-8099 
"9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" 
       TCGA-FP-8209        TCGA-FP-8210        TCGA-FP-8631        TCGA-HJ-7597 
"9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" 
       TCGA-IN-7806        TCGA-IN-7808        TCGA-IP-7968 
"9Q GAIN WILD-TYPE"       "9Q GAIN CNV" "9Q GAIN WILD-TYPE" 
       TCGA-B7-5816        TCGA-B7-5818        TCGA-BR-6452        TCGA-BR-6455 
"9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" 
       TCGA-BR-6457        TCGA-BR-6458        TCGA-BR-6563        TCGA-BR-6564 
"9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" 
       TCGA-BR-6565        TCGA-BR-6566        TCGA-BR-6705        TCGA-BR-6706 
"9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" 
       TCGA-BR-6707        TCGA-BR-6709        TCGA-BR-6710        TCGA-BR-6801 
      "9Q GAIN CNV" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" 
       TCGA-BR-6802        TCGA-BR-6803        TCGA-BR-6852        TCGA-BR-7196 
"9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" 
       TCGA-BR-7197        TCGA-BR-7703        TCGA-BR-7704        TCGA-BR-7707 
"9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE"       "9Q GAIN CNV"       "9Q GAIN CNV" 
       TCGA-BR-7715        TCGA-BR-7716        TCGA-BR-7717        TCGA-BR-7722 
"9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" 
       TCGA-BR-7723        TCGA-BR-7851        TCGA-BR-7901        TCGA-BR-7957 
"9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" 
       TCGA-BR-7958        TCGA-BR-7959        TCGA-BR-8059        TCGA-BR-8060 
"9Q GAIN WILD-TYPE"       "9Q GAIN CNV" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" 
       TCGA-BR-8077        TCGA-BR-8078        TCGA-BR-8080        TCGA-BR-8081 
"9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" 
       TCGA-BR-8284        TCGA-BR-8285        TCGA-BR-8286        TCGA-BR-8289 
"9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE"       "9Q GAIN CNV" 
       TCGA-BR-8291        TCGA-BR-8295        TCGA-BR-8296        TCGA-BR-8297 
"9Q GAIN WILD-TYPE"       "9Q GAIN CNV" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" 
       TCGA-BR-8592        TCGA-BR-A4IU        TCGA-BR-A4IV        TCGA-BR-A4IY 
"9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" 
       TCGA-BR-A4IZ        TCGA-BR-A4J1        TCGA-BR-A4J2        TCGA-BR-A4J4 
"9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE"       "9Q GAIN CNV" 
       TCGA-BR-A4J5        TCGA-BR-A4J6        TCGA-BR-A4J8        TCGA-BR-A4J9 
"9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE"       "9Q GAIN CNV" 
       TCGA-BR-A4PF        TCGA-BR-A4QI        TCGA-BR-A4QL        TCGA-CD-5798 
"9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" 
       TCGA-CD-5799        TCGA-CD-5800        TCGA-CD-5801        TCGA-CD-5802 
"9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" 
       TCGA-CD-5803        TCGA-CG-4300        TCGA-CG-4301        TCGA-CG-4304 
"9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" 
       TCGA-CG-4305        TCGA-CG-4306        TCGA-CG-4436        TCGA-CG-4437 
"9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE"       "9Q GAIN CNV" "9Q GAIN WILD-TYPE" 
       TCGA-CG-4438        TCGA-CG-4440        TCGA-CG-4441        TCGA-CG-4443 
"9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" 
       TCGA-CG-4444        TCGA-CG-4449        TCGA-CG-4455        TCGA-CG-4460 
"9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" 
       TCGA-CG-4462        TCGA-CG-4465        TCGA-CG-4466        TCGA-CG-4469 
"9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" 
       TCGA-CG-4472        TCGA-CG-4474        TCGA-CG-4477        TCGA-CG-5716 
"9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" 
       TCGA-CG-5717        TCGA-CG-5718        TCGA-CG-5719        TCGA-CG-5720 
"9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" 
       TCGA-CG-5721        TCGA-CG-5722        TCGA-CG-5723        TCGA-CG-5724 
"9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" 
       TCGA-CG-5725        TCGA-CG-5726        TCGA-CG-5727        TCGA-CG-5728 
"9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" 
       TCGA-CG-5730        TCGA-CG-5732        TCGA-CG-5733        TCGA-CG-5734 
"9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" 
       TCGA-D7-5577        TCGA-D7-5578        TCGA-D7-5579        TCGA-D7-6518 
"9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" 
       TCGA-D7-6519        TCGA-D7-6520        TCGA-D7-6521        TCGA-D7-6522 
"9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" 
       TCGA-D7-6524        TCGA-D7-6525        TCGA-D7-6526        TCGA-D7-6527 
"9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" 
       TCGA-D7-6528        TCGA-D7-6815        TCGA-D7-6817        TCGA-D7-6818 
      "9Q GAIN CNV" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE"       "9Q GAIN CNV" 
       TCGA-D7-6820        TCGA-D7-6822        TCGA-EQ-5647        TCGA-EQ-8122 
"9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE"       "9Q GAIN CNV" "9Q GAIN WILD-TYPE" 
       TCGA-F1-6177        TCGA-F1-6874        TCGA-F1-6875        TCGA-FP-7735 
"9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE"       "9Q GAIN CNV" 
       TCGA-FP-7829        TCGA-FP-7916        TCGA-FP-7998        TCGA-FP-8099 
"9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" 
       TCGA-FP-8209        TCGA-FP-8210        TCGA-FP-8631        TCGA-HJ-7597 
"9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" 
       TCGA-IN-7806        TCGA-IN-7808        TCGA-IP-7968 
"9Q GAIN WILD-TYPE"       "9Q GAIN CNV" "9Q GAIN WILD-TYPE" 
[1] "hr=" "1.1"
D17V2, continuous
D17V3, binary
[1] "tbl2"
                   cls
clus                [,1] [,2]
  9Q GAIN CNV          8   12
  9Q GAIN WILD-TYPE   64   96
        clus
vv       9Q GAIN CNV 9Q GAIN WILD-TYPE
  FEMALE           8                64
  MALE            12                96
                   vv
clus                STOMACH  ADENOCARCINOMA  DIFFUSE TYPE
  9Q GAIN CNV                                           0
  9Q GAIN WILD-TYPE                                    10
                   vv
clus                STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  9Q GAIN CNV                                                            3
  9Q GAIN WILD-TYPE                                                     13
                   vv
clus                STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  9Q GAIN CNV                                                                       1
  9Q GAIN WILD-TYPE                                                                 7
                   vv
clus                STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE
  9Q GAIN CNV                                                              1
  9Q GAIN WILD-TYPE                                                        2
                   vv
clus                STOMACH ADENOCARCINOMA  SIGNET RING TYPE
  9Q GAIN CNV                                              0
  9Q GAIN WILD-TYPE                                        1
                   vv
clus                STOMACH ADENOCARCINOMA - DIFFUSE TYPE
  9Q GAIN CNV                                           2
  9Q GAIN WILD-TYPE                                    14
                   vv
clus                STOMACH ADENOCARCINOMA - NOT OTHERWISE SPECIFIED (NOS)
  9Q GAIN CNV                                                            9
  9Q GAIN WILD-TYPE                                                     64
                   vv
clus                STOMACH INTESTINAL ADENOCARCINOMA - MUCINOUS TYPE
  9Q GAIN CNV                                                       0
  9Q GAIN WILD-TYPE                                                 7
                   vv
clus                STOMACH INTESTINAL ADENOCARCINOMA - PAPILLARY TYPE
  9Q GAIN CNV                                                        0
  9Q GAIN WILD-TYPE                                                  3
                   vv
clus                STOMACH INTESTINAL ADENOCARCINOMA - TUBULAR TYPE
  9Q GAIN CNV                                                      1
  9Q GAIN WILD-TYPE                                                9
                   vv
clus                STOMACH INTESTINAL ADENOCARCINOMA - TYPE NOT OTHERWISE SPECIFIED (NOS)
  9Q GAIN CNV                                                                            3
  9Q GAIN WILD-TYPE                                                                     25
D17V4, multiclass
                   vv
clus                T1 T2 T3 T4
  9Q GAIN CNV        2  5  5  1
  9Q GAIN WILD-TYPE  4 47 51 17
D17V5, multiclass
    clus
vv   9Q GAIN CNV 9Q GAIN WILD-TYPE
  T1           2                 4
  T2           5                47
  T3           5                51
  T4           1                17
                   vv
clus                N0 N1 N2 N3
  9Q GAIN CNV        7  4  0  3
  9Q GAIN WILD-TYPE 37 45 23 12
D17V6, multiclass
    clus
vv   9Q GAIN CNV 9Q GAIN WILD-TYPE
  N0           7                37
  N1           4                45
  N2           0                23
  N3           3                12
                   vv
clus                 M0  M1  MX
  9Q GAIN CNV        12   2   1
  9Q GAIN WILD-TYPE 106  14   7
D17V7, multiclass
    clus
vv   9Q GAIN CNV 9Q GAIN WILD-TYPE
  M0          12               106
  M1           2                14
  MX           1                 7
                   vv
clus                 I II III IV
  9Q GAIN CNV        5  3   2  2
  9Q GAIN WILD-TYPE 19 34  37 24
D17V8, multiclass
     clus
vv    9Q GAIN CNV 9Q GAIN WILD-TYPE
  I             5                19
  II            3                34
  III           2                37
  IV            2                24
D17V9, binary
[1] "tbl2"
                   cls
clus                [,1] [,2]
  9Q GAIN CNV          1   19
  9Q GAIN WILD-TYPE    4  156
     clus
vv    9Q GAIN CNV 9Q GAIN WILD-TYPE
  NO            1                 4
  YES          19               156
                   vv
clus                 R0  R1  R2  RX
  9Q GAIN CNV        15   0   1   3
  9Q GAIN WILD-TYPE 110   7  11  22
D17V10, multiclass
    clus
vv   9Q GAIN CNV 9Q GAIN WILD-TYPE
  R0          15               110
  R1           0                 7
  R2           1                11
  RX           3                22
D17V11, continuous

Clustering(18) Variable = 10p gain
D18V1, survival
                    sevent
clus2                  0   1
  10P GAIN CNV        20   4
  10P GAIN WILD-TYPE 104  15
      10P GAIN CNV 10P GAIN WILD-TYPE 
                24                119 
      10P GAIN CNV 10P GAIN WILD-TYPE 
                 4                 15 
$`10P GAIN CNV`
TCGA-BR-6565 TCGA-BR-6801 TCGA-BR-7197 TCGA-BR-7715 TCGA-BR-7716 TCGA-BR-7717 
        0.62         1.12         1.48         1.05         0.82         0.69 
TCGA-BR-7723 TCGA-BR-8289 TCGA-BR-8295 TCGA-BR-A4J8 TCGA-BR-A4PF TCGA-BR-A4QI 
        4.54         0.26         1.55         0.23         0.72         0.49 
TCGA-CD-5801 TCGA-CG-4300 TCGA-CG-4440 TCGA-CG-4444 TCGA-CG-4460 TCGA-CG-4472 
        0.49        20.02         4.01        47.05        21.99        12.00 
TCGA-CG-5730 TCGA-D7-6518 TCGA-D7-6520 TCGA-EQ-5647 TCGA-F1-6875 TCGA-FP-7735 
        4.01         9.80         9.63         0.62        72.23         0.39 

$`10P GAIN WILD-TYPE`
TCGA-B7-5816 TCGA-B7-5818 TCGA-BR-6452 TCGA-BR-6455 TCGA-BR-6457 TCGA-BR-6458 
        5.62         0.10         0.95         1.41         1.35         1.35 
TCGA-BR-6563 TCGA-BR-6564 TCGA-BR-6566 TCGA-BR-6705 TCGA-BR-6706 TCGA-BR-6707 
        0.85         0.82         0.62         1.71         2.17         0.99 
TCGA-BR-6709 TCGA-BR-6710 TCGA-BR-6802 TCGA-BR-6803 TCGA-BR-6852 TCGA-BR-7196 
        1.22         0.66         0.76         0.66         0.26         1.22 
TCGA-BR-7703 TCGA-BR-7704 TCGA-BR-7707 TCGA-BR-7722 TCGA-BR-7851 TCGA-BR-7901 
        0.46         1.25         0.13         0.16         0.99         0.95 
TCGA-BR-7957 TCGA-BR-7958 TCGA-BR-7959 TCGA-BR-8059 TCGA-BR-8060 TCGA-BR-8077 
        0.69         0.16         1.08         0.82         1.32         0.69 
TCGA-BR-8078 TCGA-BR-8080 TCGA-BR-8081 TCGA-BR-8284 TCGA-BR-8285 TCGA-BR-8286 
        0.95         0.49         0.46         0.72         0.26         0.43 
TCGA-BR-8291 TCGA-BR-8296 TCGA-BR-8297 TCGA-BR-8592 TCGA-BR-A4IU TCGA-BR-A4IV 
        1.18         1.48         0.76         0.20         0.59         0.92 
TCGA-BR-A4IY TCGA-BR-A4IZ TCGA-BR-A4J1 TCGA-BR-A4J2 TCGA-BR-A4J4 TCGA-BR-A4J5 
        0.39         0.79         0.72         0.79         0.53         0.43 
TCGA-BR-A4J6 TCGA-BR-A4J9 TCGA-BR-A4QL TCGA-CD-5798 TCGA-CD-5799 TCGA-CD-5800 
        0.13         0.10         2.24         0.82         0.69         0.36 
TCGA-CD-5802 TCGA-CD-5803 TCGA-CG-4301 TCGA-CG-4304 TCGA-CG-4305 TCGA-CG-4306 
        0.30         0.07         3.02        27.02        15.95         1.02 
TCGA-CG-4436 TCGA-CG-4437 TCGA-CG-4438 TCGA-CG-4441 TCGA-CG-4443 TCGA-CG-4449 
       52.96         8.05        54.05        14.01        29.98        19.07 
TCGA-CG-4455 TCGA-CG-4462 TCGA-CG-4465 TCGA-CG-4466 TCGA-CG-4469 TCGA-CG-4474 
       12.03         1.02         8.98        18.94         7.07         1.02 
TCGA-CG-4477 TCGA-CG-5716 TCGA-CG-5717 TCGA-CG-5718 TCGA-CG-5719 TCGA-CG-5720 
        1.02         1.02         6.94         1.02         1.02         0.99 
TCGA-CG-5721 TCGA-CG-5722 TCGA-CG-5723 TCGA-CG-5724 TCGA-CG-5725 TCGA-CG-5726 
        5.98         0.95        70.06        12.03        15.02        28.96 
TCGA-CG-5727 TCGA-CG-5728 TCGA-CG-5732 TCGA-CG-5733 TCGA-CG-5734 TCGA-D7-5577 
       31.04        65.10        55.04        21.07         7.99         8.65 
TCGA-D7-5578 TCGA-D7-5579 TCGA-D7-6519 TCGA-D7-6521 TCGA-D7-6522 TCGA-D7-6524 
        3.58         4.54        15.65         8.19         6.90         0.69 
TCGA-D7-6525 TCGA-D7-6526 TCGA-D7-6527 TCGA-D7-6528 TCGA-D7-6815 TCGA-D7-6817 
        5.95         6.61         4.14         1.68         3.65         4.70 
TCGA-D7-6818 TCGA-D7-6820 TCGA-D7-6822 TCGA-EQ-8122 TCGA-F1-6177 TCGA-F1-6874 
        4.04         2.93         4.27         7.79         6.54         2.01 
TCGA-FP-7829 TCGA-FP-7916 TCGA-FP-7998 TCGA-FP-8099 TCGA-FP-8209 TCGA-FP-8210 
        0.20         3.02         3.58         1.02        59.05         5.03 
TCGA-FP-8631 TCGA-HJ-7597 TCGA-IN-7806 TCGA-IN-7808 TCGA-IP-7968 
        0.56        26.43         6.87         3.55         2.53 

      10P GAIN CNV 10P GAIN WILD-TYPE 
              0.23               0.07 
      10P GAIN CNV 10P GAIN WILD-TYPE 
             72.23              70.06 
      10P GAIN CNV 10P GAIN WILD-TYPE 
              1.30               1.25 
[1] "0.2 - 72.2 (1.3)" "0.1 - 70.1 (1.2)"
        TCGA-B7-5816         TCGA-B7-5818         TCGA-BR-6452 
"10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" 
        TCGA-BR-6455         TCGA-BR-6457         TCGA-BR-6458 
"10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" 
        TCGA-BR-6563         TCGA-BR-6564         TCGA-BR-6565 
"10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE"       "10P GAIN CNV" 
        TCGA-BR-6566         TCGA-BR-6705         TCGA-BR-6706 
"10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" 
        TCGA-BR-6707         TCGA-BR-6709         TCGA-BR-6710 
"10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" 
        TCGA-BR-6801         TCGA-BR-6802         TCGA-BR-6803 
      "10P GAIN CNV" "10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" 
        TCGA-BR-6852         TCGA-BR-7196         TCGA-BR-7197 
"10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE"       "10P GAIN CNV" 
        TCGA-BR-7703         TCGA-BR-7704         TCGA-BR-7707 
"10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" 
        TCGA-BR-7715         TCGA-BR-7716         TCGA-BR-7717 
      "10P GAIN CNV"       "10P GAIN CNV"       "10P GAIN CNV" 
        TCGA-BR-7722         TCGA-BR-7723         TCGA-BR-7851 
"10P GAIN WILD-TYPE"       "10P GAIN CNV" "10P GAIN WILD-TYPE" 
        TCGA-BR-7901         TCGA-BR-7957         TCGA-BR-7958 
"10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" 
        TCGA-BR-7959         TCGA-BR-8059         TCGA-BR-8060 
"10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" 
        TCGA-BR-8077         TCGA-BR-8078         TCGA-BR-8080 
"10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" 
        TCGA-BR-8081         TCGA-BR-8284         TCGA-BR-8285 
"10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" 
        TCGA-BR-8286         TCGA-BR-8289         TCGA-BR-8291 
"10P GAIN WILD-TYPE"       "10P GAIN CNV" "10P GAIN WILD-TYPE" 
        TCGA-BR-8295         TCGA-BR-8296         TCGA-BR-8297 
      "10P GAIN CNV" "10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" 
        TCGA-BR-8592         TCGA-BR-A4IU         TCGA-BR-A4IV 
"10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" 
        TCGA-BR-A4IY         TCGA-BR-A4IZ         TCGA-BR-A4J1 
"10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" 
        TCGA-BR-A4J2         TCGA-BR-A4J4         TCGA-BR-A4J5 
"10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" 
        TCGA-BR-A4J6         TCGA-BR-A4J8         TCGA-BR-A4J9 
"10P GAIN WILD-TYPE"       "10P GAIN CNV" "10P GAIN WILD-TYPE" 
        TCGA-BR-A4PF         TCGA-BR-A4QI         TCGA-BR-A4QL 
      "10P GAIN CNV"       "10P GAIN CNV" "10P GAIN WILD-TYPE" 
        TCGA-CD-5798         TCGA-CD-5799         TCGA-CD-5800 
"10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" 
        TCGA-CD-5801         TCGA-CD-5802         TCGA-CD-5803 
      "10P GAIN CNV" "10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" 
        TCGA-CG-4300         TCGA-CG-4301         TCGA-CG-4304 
      "10P GAIN CNV" "10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" 
        TCGA-CG-4305         TCGA-CG-4306         TCGA-CG-4436 
"10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" 
        TCGA-CG-4437         TCGA-CG-4438         TCGA-CG-4440 
"10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE"       "10P GAIN CNV" 
        TCGA-CG-4441         TCGA-CG-4443         TCGA-CG-4444 
"10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE"       "10P GAIN CNV" 
        TCGA-CG-4449         TCGA-CG-4455         TCGA-CG-4460 
"10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE"       "10P GAIN CNV" 
        TCGA-CG-4462         TCGA-CG-4465         TCGA-CG-4466 
"10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" 
        TCGA-CG-4469         TCGA-CG-4472         TCGA-CG-4474 
"10P GAIN WILD-TYPE"       "10P GAIN CNV" "10P GAIN WILD-TYPE" 
        TCGA-CG-4477         TCGA-CG-5716         TCGA-CG-5717 
"10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" 
        TCGA-CG-5718         TCGA-CG-5719         TCGA-CG-5720 
"10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" 
        TCGA-CG-5721         TCGA-CG-5722         TCGA-CG-5723 
"10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" 
        TCGA-CG-5724         TCGA-CG-5725         TCGA-CG-5726 
"10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" 
        TCGA-CG-5727         TCGA-CG-5728         TCGA-CG-5730 
"10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE"       "10P GAIN CNV" 
        TCGA-CG-5732         TCGA-CG-5733         TCGA-CG-5734 
"10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" 
        TCGA-D7-5577         TCGA-D7-5578         TCGA-D7-5579 
"10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" 
        TCGA-D7-6518         TCGA-D7-6519         TCGA-D7-6520 
      "10P GAIN CNV" "10P GAIN WILD-TYPE"       "10P GAIN CNV" 
        TCGA-D7-6521         TCGA-D7-6522         TCGA-D7-6524 
"10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" 
        TCGA-D7-6525         TCGA-D7-6526         TCGA-D7-6527 
"10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" 
        TCGA-D7-6528         TCGA-D7-6815         TCGA-D7-6817 
"10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" 
        TCGA-D7-6818         TCGA-D7-6820         TCGA-D7-6822 
"10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" 
        TCGA-EQ-5647         TCGA-EQ-8122         TCGA-F1-6177 
      "10P GAIN CNV" "10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" 
        TCGA-F1-6874         TCGA-F1-6875         TCGA-FP-7735 
"10P GAIN WILD-TYPE"       "10P GAIN CNV"       "10P GAIN CNV" 
        TCGA-FP-7829         TCGA-FP-7916         TCGA-FP-7998 
"10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" 
        TCGA-FP-8099         TCGA-FP-8209         TCGA-FP-8210 
"10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" 
        TCGA-FP-8631         TCGA-HJ-7597         TCGA-IN-7806 
"10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" 
        TCGA-IN-7808         TCGA-IP-7968 
"10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" 
        TCGA-B7-5816         TCGA-B7-5818         TCGA-BR-6452 
"10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" 
        TCGA-BR-6455         TCGA-BR-6457         TCGA-BR-6458 
"10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" 
        TCGA-BR-6563         TCGA-BR-6564         TCGA-BR-6565 
"10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE"       "10P GAIN CNV" 
        TCGA-BR-6566         TCGA-BR-6705         TCGA-BR-6706 
"10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" 
        TCGA-BR-6707         TCGA-BR-6709         TCGA-BR-6710 
"10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" 
        TCGA-BR-6801         TCGA-BR-6802         TCGA-BR-6803 
      "10P GAIN CNV" "10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" 
        TCGA-BR-6852         TCGA-BR-7196         TCGA-BR-7197 
"10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE"       "10P GAIN CNV" 
        TCGA-BR-7703         TCGA-BR-7704         TCGA-BR-7707 
"10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" 
        TCGA-BR-7715         TCGA-BR-7716         TCGA-BR-7717 
      "10P GAIN CNV"       "10P GAIN CNV"       "10P GAIN CNV" 
        TCGA-BR-7722         TCGA-BR-7723         TCGA-BR-7851 
"10P GAIN WILD-TYPE"       "10P GAIN CNV" "10P GAIN WILD-TYPE" 
        TCGA-BR-7901         TCGA-BR-7957         TCGA-BR-7958 
"10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" 
        TCGA-BR-7959         TCGA-BR-8059         TCGA-BR-8060 
"10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" 
        TCGA-BR-8077         TCGA-BR-8078         TCGA-BR-8080 
"10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" 
        TCGA-BR-8081         TCGA-BR-8284         TCGA-BR-8285 
"10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" 
        TCGA-BR-8286         TCGA-BR-8289         TCGA-BR-8291 
"10P GAIN WILD-TYPE"       "10P GAIN CNV" "10P GAIN WILD-TYPE" 
        TCGA-BR-8295         TCGA-BR-8296         TCGA-BR-8297 
      "10P GAIN CNV" "10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" 
        TCGA-BR-8592         TCGA-BR-A4IU         TCGA-BR-A4IV 
"10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" 
        TCGA-BR-A4IY         TCGA-BR-A4IZ         TCGA-BR-A4J1 
"10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" 
        TCGA-BR-A4J2         TCGA-BR-A4J4         TCGA-BR-A4J5 
"10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" 
        TCGA-BR-A4J6         TCGA-BR-A4J8         TCGA-BR-A4J9 
"10P GAIN WILD-TYPE"       "10P GAIN CNV" "10P GAIN WILD-TYPE" 
        TCGA-BR-A4PF         TCGA-BR-A4QI         TCGA-BR-A4QL 
      "10P GAIN CNV"       "10P GAIN CNV" "10P GAIN WILD-TYPE" 
        TCGA-CD-5798         TCGA-CD-5799         TCGA-CD-5800 
"10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" 
        TCGA-CD-5801         TCGA-CD-5802         TCGA-CD-5803 
      "10P GAIN CNV" "10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" 
        TCGA-CG-4300         TCGA-CG-4301         TCGA-CG-4304 
      "10P GAIN CNV" "10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" 
        TCGA-CG-4305         TCGA-CG-4306         TCGA-CG-4436 
"10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" 
        TCGA-CG-4437         TCGA-CG-4438         TCGA-CG-4440 
"10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE"       "10P GAIN CNV" 
        TCGA-CG-4441         TCGA-CG-4443         TCGA-CG-4444 
"10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE"       "10P GAIN CNV" 
        TCGA-CG-4449         TCGA-CG-4455         TCGA-CG-4460 
"10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE"       "10P GAIN CNV" 
        TCGA-CG-4462         TCGA-CG-4465         TCGA-CG-4466 
"10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" 
        TCGA-CG-4469         TCGA-CG-4472         TCGA-CG-4474 
"10P GAIN WILD-TYPE"       "10P GAIN CNV" "10P GAIN WILD-TYPE" 
        TCGA-CG-4477         TCGA-CG-5716         TCGA-CG-5717 
"10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" 
        TCGA-CG-5718         TCGA-CG-5719         TCGA-CG-5720 
"10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" 
        TCGA-CG-5721         TCGA-CG-5722         TCGA-CG-5723 
"10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" 
        TCGA-CG-5724         TCGA-CG-5725         TCGA-CG-5726 
"10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" 
        TCGA-CG-5727         TCGA-CG-5728         TCGA-CG-5730 
"10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE"       "10P GAIN CNV" 
        TCGA-CG-5732         TCGA-CG-5733         TCGA-CG-5734 
"10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" 
        TCGA-D7-5577         TCGA-D7-5578         TCGA-D7-5579 
"10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" 
        TCGA-D7-6518         TCGA-D7-6519         TCGA-D7-6520 
      "10P GAIN CNV" "10P GAIN WILD-TYPE"       "10P GAIN CNV" 
        TCGA-D7-6521         TCGA-D7-6522         TCGA-D7-6524 
"10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" 
        TCGA-D7-6525         TCGA-D7-6526         TCGA-D7-6527 
"10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" 
        TCGA-D7-6528         TCGA-D7-6815         TCGA-D7-6817 
"10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" 
        TCGA-D7-6818         TCGA-D7-6820         TCGA-D7-6822 
"10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" 
        TCGA-EQ-5647         TCGA-EQ-8122         TCGA-F1-6177 
      "10P GAIN CNV" "10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" 
        TCGA-F1-6874         TCGA-F1-6875         TCGA-FP-7735 
"10P GAIN WILD-TYPE"       "10P GAIN CNV"       "10P GAIN CNV" 
        TCGA-FP-7829         TCGA-FP-7916         TCGA-FP-7998 
"10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" 
        TCGA-FP-8099         TCGA-FP-8209         TCGA-FP-8210 
"10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" 
        TCGA-FP-8631         TCGA-HJ-7597         TCGA-IN-7806 
"10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" 
        TCGA-IN-7808         TCGA-IP-7968 
"10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" 
        TCGA-B7-5816         TCGA-B7-5818         TCGA-BR-6452 
"10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" 
        TCGA-BR-6455         TCGA-BR-6457         TCGA-BR-6458 
"10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" 
        TCGA-BR-6563         TCGA-BR-6564         TCGA-BR-6565 
"10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE"       "10P GAIN CNV" 
        TCGA-BR-6566         TCGA-BR-6705         TCGA-BR-6706 
"10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" 
        TCGA-BR-6707         TCGA-BR-6709         TCGA-BR-6710 
"10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" 
        TCGA-BR-6801         TCGA-BR-6802         TCGA-BR-6803 
      "10P GAIN CNV" "10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" 
        TCGA-BR-6852         TCGA-BR-7196         TCGA-BR-7197 
"10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE"       "10P GAIN CNV" 
        TCGA-BR-7703         TCGA-BR-7704         TCGA-BR-7707 
"10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" 
        TCGA-BR-7715         TCGA-BR-7716         TCGA-BR-7717 
      "10P GAIN CNV"       "10P GAIN CNV"       "10P GAIN CNV" 
        TCGA-BR-7722         TCGA-BR-7723         TCGA-BR-7851 
"10P GAIN WILD-TYPE"       "10P GAIN CNV" "10P GAIN WILD-TYPE" 
        TCGA-BR-7901         TCGA-BR-7957         TCGA-BR-7958 
"10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" 
        TCGA-BR-7959         TCGA-BR-8059         TCGA-BR-8060 
"10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" 
        TCGA-BR-8077         TCGA-BR-8078         TCGA-BR-8080 
"10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" 
        TCGA-BR-8081         TCGA-BR-8284         TCGA-BR-8285 
"10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" 
        TCGA-BR-8286         TCGA-BR-8289         TCGA-BR-8291 
"10P GAIN WILD-TYPE"       "10P GAIN CNV" "10P GAIN WILD-TYPE" 
        TCGA-BR-8295         TCGA-BR-8296         TCGA-BR-8297 
      "10P GAIN CNV" "10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" 
        TCGA-BR-8592         TCGA-BR-A4IU         TCGA-BR-A4IV 
"10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" 
        TCGA-BR-A4IY         TCGA-BR-A4IZ         TCGA-BR-A4J1 
"10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" 
        TCGA-BR-A4J2         TCGA-BR-A4J4         TCGA-BR-A4J5 
"10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" 
        TCGA-BR-A4J6         TCGA-BR-A4J8         TCGA-BR-A4J9 
"10P GAIN WILD-TYPE"       "10P GAIN CNV" "10P GAIN WILD-TYPE" 
        TCGA-BR-A4PF         TCGA-BR-A4QI         TCGA-BR-A4QL 
      "10P GAIN CNV"       "10P GAIN CNV" "10P GAIN WILD-TYPE" 
        TCGA-CD-5798         TCGA-CD-5799         TCGA-CD-5800 
"10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" 
        TCGA-CD-5801         TCGA-CD-5802         TCGA-CD-5803 
      "10P GAIN CNV" "10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" 
        TCGA-CG-4300         TCGA-CG-4301         TCGA-CG-4304 
      "10P GAIN CNV" "10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" 
        TCGA-CG-4305         TCGA-CG-4306         TCGA-CG-4436 
"10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" 
        TCGA-CG-4437         TCGA-CG-4438         TCGA-CG-4440 
"10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE"       "10P GAIN CNV" 
        TCGA-CG-4441         TCGA-CG-4443         TCGA-CG-4444 
"10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE"       "10P GAIN CNV" 
        TCGA-CG-4449         TCGA-CG-4455         TCGA-CG-4460 
"10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE"       "10P GAIN CNV" 
        TCGA-CG-4462         TCGA-CG-4465         TCGA-CG-4466 
"10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" 
        TCGA-CG-4469         TCGA-CG-4472         TCGA-CG-4474 
"10P GAIN WILD-TYPE"       "10P GAIN CNV" "10P GAIN WILD-TYPE" 
        TCGA-CG-4477         TCGA-CG-5716         TCGA-CG-5717 
"10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" 
        TCGA-CG-5718         TCGA-CG-5719         TCGA-CG-5720 
"10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" 
        TCGA-CG-5721         TCGA-CG-5722         TCGA-CG-5723 
"10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" 
        TCGA-CG-5724         TCGA-CG-5725         TCGA-CG-5726 
"10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" 
        TCGA-CG-5727         TCGA-CG-5728         TCGA-CG-5730 
"10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE"       "10P GAIN CNV" 
        TCGA-CG-5732         TCGA-CG-5733         TCGA-CG-5734 
"10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" 
        TCGA-D7-5577         TCGA-D7-5578         TCGA-D7-5579 
"10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" 
        TCGA-D7-6518         TCGA-D7-6519         TCGA-D7-6520 
      "10P GAIN CNV" "10P GAIN WILD-TYPE"       "10P GAIN CNV" 
        TCGA-D7-6521         TCGA-D7-6522         TCGA-D7-6524 
"10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" 
        TCGA-D7-6525         TCGA-D7-6526         TCGA-D7-6527 
"10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" 
        TCGA-D7-6528         TCGA-D7-6815         TCGA-D7-6817 
"10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" 
        TCGA-D7-6818         TCGA-D7-6820         TCGA-D7-6822 
"10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" 
        TCGA-EQ-5647         TCGA-EQ-8122         TCGA-F1-6177 
      "10P GAIN CNV" "10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" 
        TCGA-F1-6874         TCGA-F1-6875         TCGA-FP-7735 
"10P GAIN WILD-TYPE"       "10P GAIN CNV"       "10P GAIN CNV" 
        TCGA-FP-7829         TCGA-FP-7916         TCGA-FP-7998 
"10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" 
        TCGA-FP-8099         TCGA-FP-8209         TCGA-FP-8210 
"10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" 
        TCGA-FP-8631         TCGA-HJ-7597         TCGA-IN-7806 
"10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" 
        TCGA-IN-7808         TCGA-IP-7968 
"10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" 
[1] "hr=" "1.2"
D18V2, continuous
D18V3, binary
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  10P GAIN CNV         11   18
  10P GAIN WILD-TYPE   61   90
        clus
vv       10P GAIN CNV 10P GAIN WILD-TYPE
  FEMALE           11                 61
  MALE             18                 90
                    vv
clus                 STOMACH  ADENOCARCINOMA  DIFFUSE TYPE
  10P GAIN CNV                                           0
  10P GAIN WILD-TYPE                                    10
                    vv
clus                 STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  10P GAIN CNV                                                            4
  10P GAIN WILD-TYPE                                                     12
                    vv
clus                 STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  10P GAIN CNV                                                                       1
  10P GAIN WILD-TYPE                                                                 7
                    vv
clus                 STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE
  10P GAIN CNV                                                              0
  10P GAIN WILD-TYPE                                                        3
                    vv
clus                 STOMACH ADENOCARCINOMA  SIGNET RING TYPE
  10P GAIN CNV                                              0
  10P GAIN WILD-TYPE                                        1
                    vv
clus                 STOMACH ADENOCARCINOMA - DIFFUSE TYPE
  10P GAIN CNV                                           1
  10P GAIN WILD-TYPE                                    15
                    vv
clus                 STOMACH ADENOCARCINOMA - NOT OTHERWISE SPECIFIED (NOS)
  10P GAIN CNV                                                           17
  10P GAIN WILD-TYPE                                                     56
                    vv
clus                 STOMACH INTESTINAL ADENOCARCINOMA - MUCINOUS TYPE
  10P GAIN CNV                                                       0
  10P GAIN WILD-TYPE                                                 7
                    vv
clus                 STOMACH INTESTINAL ADENOCARCINOMA - PAPILLARY TYPE
  10P GAIN CNV                                                        0
  10P GAIN WILD-TYPE                                                  3
                    vv
clus                 STOMACH INTESTINAL ADENOCARCINOMA - TUBULAR TYPE
  10P GAIN CNV                                                      1
  10P GAIN WILD-TYPE                                                9
                    vv
clus                 STOMACH INTESTINAL ADENOCARCINOMA - TYPE NOT OTHERWISE SPECIFIED (NOS)
  10P GAIN CNV                                                                            3
  10P GAIN WILD-TYPE                                                                     25
D18V4, multiclass
                    vv
clus                 T1 T2 T3 T4
  10P GAIN CNV        0  6 10  7
  10P GAIN WILD-TYPE  6 46 46 11
D18V5, multiclass
    clus
vv   10P GAIN CNV 10P GAIN WILD-TYPE
  T1            0                  6
  T2            6                 46
  T3           10                 46
  T4            7                 11
                    vv
clus                 N0 N1 N2 N3
  10P GAIN CNV        6  9  5  3
  10P GAIN WILD-TYPE 38 40 18 12
D18V6, multiclass
    clus
vv   10P GAIN CNV 10P GAIN WILD-TYPE
  N0            6                 38
  N1            9                 40
  N2            5                 18
  N3            3                 12
                    vv
clus                  M0  M1  MX
  10P GAIN CNV        18   4   2
  10P GAIN WILD-TYPE 100  12   6
D18V7, multiclass
    clus
vv   10P GAIN CNV 10P GAIN WILD-TYPE
  M0           18                100
  M1            4                 12
  MX            2                  6
                    vv
clus                  I II III IV
  10P GAIN CNV        2  5   6  9
  10P GAIN WILD-TYPE 22 32  33 17
D18V8, multiclass
     clus
vv    10P GAIN CNV 10P GAIN WILD-TYPE
  I              2                 22
  II             5                 32
  III            6                 33
  IV             9                 17
D18V9, binary
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  10P GAIN CNV          0   29
  10P GAIN WILD-TYPE    5  146
     clus
vv    10P GAIN CNV 10P GAIN WILD-TYPE
  NO             0                  5
  YES           29                146
                    vv
clus                  R0  R1  R2  RX
  10P GAIN CNV        19   1   4   4
  10P GAIN WILD-TYPE 106   6   8  21
D18V10, multiclass
    clus
vv   10P GAIN CNV 10P GAIN WILD-TYPE
  R0           19                106
  R1            1                  6
  R2            4                  8
  RX            4                 21
D18V11, continuous

Clustering(19) Variable = 10q gain
D19V1, survival
                    sevent
clus2                  0   1
  10Q GAIN CNV         9   3
  10Q GAIN WILD-TYPE 115  16
      10Q GAIN CNV 10Q GAIN WILD-TYPE 
                12                131 
      10Q GAIN CNV 10Q GAIN WILD-TYPE 
                 3                 16 
$`10Q GAIN CNV`
TCGA-BR-7197 TCGA-BR-7715 TCGA-BR-8289 TCGA-BR-A4PF TCGA-CD-5801 TCGA-CG-4444 
        1.48         1.05         0.26         0.72         0.49        47.05 
TCGA-CG-4460 TCGA-CG-4472 TCGA-D7-6520 TCGA-EQ-5647 TCGA-F1-6875 TCGA-FP-7735 
       21.99        12.00         9.63         0.62        72.23         0.39 

$`10Q GAIN WILD-TYPE`
TCGA-B7-5816 TCGA-B7-5818 TCGA-BR-6452 TCGA-BR-6455 TCGA-BR-6457 TCGA-BR-6458 
        5.62         0.10         0.95         1.41         1.35         1.35 
TCGA-BR-6563 TCGA-BR-6564 TCGA-BR-6565 TCGA-BR-6566 TCGA-BR-6705 TCGA-BR-6706 
        0.85         0.82         0.62         0.62         1.71         2.17 
TCGA-BR-6707 TCGA-BR-6709 TCGA-BR-6710 TCGA-BR-6801 TCGA-BR-6802 TCGA-BR-6803 
        0.99         1.22         0.66         1.12         0.76         0.66 
TCGA-BR-6852 TCGA-BR-7196 TCGA-BR-7703 TCGA-BR-7704 TCGA-BR-7707 TCGA-BR-7716 
        0.26         1.22         0.46         1.25         0.13         0.82 
TCGA-BR-7717 TCGA-BR-7722 TCGA-BR-7723 TCGA-BR-7851 TCGA-BR-7901 TCGA-BR-7957 
        0.69         0.16         4.54         0.99         0.95         0.69 
TCGA-BR-7958 TCGA-BR-7959 TCGA-BR-8059 TCGA-BR-8060 TCGA-BR-8077 TCGA-BR-8078 
        0.16         1.08         0.82         1.32         0.69         0.95 
TCGA-BR-8080 TCGA-BR-8081 TCGA-BR-8284 TCGA-BR-8285 TCGA-BR-8286 TCGA-BR-8291 
        0.49         0.46         0.72         0.26         0.43         1.18 
TCGA-BR-8295 TCGA-BR-8296 TCGA-BR-8297 TCGA-BR-8592 TCGA-BR-A4IU TCGA-BR-A4IV 
        1.55         1.48         0.76         0.20         0.59         0.92 
TCGA-BR-A4IY TCGA-BR-A4IZ TCGA-BR-A4J1 TCGA-BR-A4J2 TCGA-BR-A4J4 TCGA-BR-A4J5 
        0.39         0.79         0.72         0.79         0.53         0.43 
TCGA-BR-A4J6 TCGA-BR-A4J8 TCGA-BR-A4J9 TCGA-BR-A4QI TCGA-BR-A4QL TCGA-CD-5798 
        0.13         0.23         0.10         0.49         2.24         0.82 
TCGA-CD-5799 TCGA-CD-5800 TCGA-CD-5802 TCGA-CD-5803 TCGA-CG-4300 TCGA-CG-4301 
        0.69         0.36         0.30         0.07        20.02         3.02 
TCGA-CG-4304 TCGA-CG-4305 TCGA-CG-4306 TCGA-CG-4436 TCGA-CG-4437 TCGA-CG-4438 
       27.02        15.95         1.02        52.96         8.05        54.05 
TCGA-CG-4440 TCGA-CG-4441 TCGA-CG-4443 TCGA-CG-4449 TCGA-CG-4455 TCGA-CG-4462 
        4.01        14.01        29.98        19.07        12.03         1.02 
TCGA-CG-4465 TCGA-CG-4466 TCGA-CG-4469 TCGA-CG-4474 TCGA-CG-4477 TCGA-CG-5716 
        8.98        18.94         7.07         1.02         1.02         1.02 
TCGA-CG-5717 TCGA-CG-5718 TCGA-CG-5719 TCGA-CG-5720 TCGA-CG-5721 TCGA-CG-5722 
        6.94         1.02         1.02         0.99         5.98         0.95 
TCGA-CG-5723 TCGA-CG-5724 TCGA-CG-5725 TCGA-CG-5726 TCGA-CG-5727 TCGA-CG-5728 
       70.06        12.03        15.02        28.96        31.04        65.10 
TCGA-CG-5730 TCGA-CG-5732 TCGA-CG-5733 TCGA-CG-5734 TCGA-D7-5577 TCGA-D7-5578 
        4.01        55.04        21.07         7.99         8.65         3.58 
TCGA-D7-5579 TCGA-D7-6518 TCGA-D7-6519 TCGA-D7-6521 TCGA-D7-6522 TCGA-D7-6524 
        4.54         9.80        15.65         8.19         6.90         0.69 
TCGA-D7-6525 TCGA-D7-6526 TCGA-D7-6527 TCGA-D7-6528 TCGA-D7-6815 TCGA-D7-6817 
        5.95         6.61         4.14         1.68         3.65         4.70 
TCGA-D7-6818 TCGA-D7-6820 TCGA-D7-6822 TCGA-EQ-8122 TCGA-F1-6177 TCGA-F1-6874 
        4.04         2.93         4.27         7.79         6.54         2.01 
TCGA-FP-7829 TCGA-FP-7916 TCGA-FP-7998 TCGA-FP-8099 TCGA-FP-8209 TCGA-FP-8210 
        0.20         3.02         3.58         1.02        59.05         5.03 
TCGA-FP-8631 TCGA-HJ-7597 TCGA-IN-7806 TCGA-IN-7808 TCGA-IP-7968 
        0.56        26.43         6.87         3.55         2.53 

      10Q GAIN CNV 10Q GAIN WILD-TYPE 
              0.26               0.07 
      10Q GAIN CNV 10Q GAIN WILD-TYPE 
             72.23              70.06 
      10Q GAIN CNV 10Q GAIN WILD-TYPE 
             1.265              1.250 
[1] "0.3 - 72.2 (1.3)" "0.1 - 70.1 (1.2)"
        TCGA-B7-5816         TCGA-B7-5818         TCGA-BR-6452 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-BR-6455         TCGA-BR-6457         TCGA-BR-6458 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-BR-6563         TCGA-BR-6564         TCGA-BR-6565 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-BR-6566         TCGA-BR-6705         TCGA-BR-6706 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-BR-6707         TCGA-BR-6709         TCGA-BR-6710 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-BR-6801         TCGA-BR-6802         TCGA-BR-6803 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-BR-6852         TCGA-BR-7196         TCGA-BR-7197 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE"       "10Q GAIN CNV" 
        TCGA-BR-7703         TCGA-BR-7704         TCGA-BR-7707 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-BR-7715         TCGA-BR-7716         TCGA-BR-7717 
      "10Q GAIN CNV" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-BR-7722         TCGA-BR-7723         TCGA-BR-7851 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-BR-7901         TCGA-BR-7957         TCGA-BR-7958 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-BR-7959         TCGA-BR-8059         TCGA-BR-8060 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-BR-8077         TCGA-BR-8078         TCGA-BR-8080 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-BR-8081         TCGA-BR-8284         TCGA-BR-8285 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-BR-8286         TCGA-BR-8289         TCGA-BR-8291 
"10Q GAIN WILD-TYPE"       "10Q GAIN CNV" "10Q GAIN WILD-TYPE" 
        TCGA-BR-8295         TCGA-BR-8296         TCGA-BR-8297 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-BR-8592         TCGA-BR-A4IU         TCGA-BR-A4IV 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-BR-A4IY         TCGA-BR-A4IZ         TCGA-BR-A4J1 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-BR-A4J2         TCGA-BR-A4J4         TCGA-BR-A4J5 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-BR-A4J6         TCGA-BR-A4J8         TCGA-BR-A4J9 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-BR-A4PF         TCGA-BR-A4QI         TCGA-BR-A4QL 
      "10Q GAIN CNV" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-CD-5798         TCGA-CD-5799         TCGA-CD-5800 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-CD-5801         TCGA-CD-5802         TCGA-CD-5803 
      "10Q GAIN CNV" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-CG-4300         TCGA-CG-4301         TCGA-CG-4304 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-CG-4305         TCGA-CG-4306         TCGA-CG-4436 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-CG-4437         TCGA-CG-4438         TCGA-CG-4440 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-CG-4441         TCGA-CG-4443         TCGA-CG-4444 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE"       "10Q GAIN CNV" 
        TCGA-CG-4449         TCGA-CG-4455         TCGA-CG-4460 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE"       "10Q GAIN CNV" 
        TCGA-CG-4462         TCGA-CG-4465         TCGA-CG-4466 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-CG-4469         TCGA-CG-4472         TCGA-CG-4474 
"10Q GAIN WILD-TYPE"       "10Q GAIN CNV" "10Q GAIN WILD-TYPE" 
        TCGA-CG-4477         TCGA-CG-5716         TCGA-CG-5717 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-CG-5718         TCGA-CG-5719         TCGA-CG-5720 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-CG-5721         TCGA-CG-5722         TCGA-CG-5723 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-CG-5724         TCGA-CG-5725         TCGA-CG-5726 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-CG-5727         TCGA-CG-5728         TCGA-CG-5730 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-CG-5732         TCGA-CG-5733         TCGA-CG-5734 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-D7-5577         TCGA-D7-5578         TCGA-D7-5579 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-D7-6518         TCGA-D7-6519         TCGA-D7-6520 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE"       "10Q GAIN CNV" 
        TCGA-D7-6521         TCGA-D7-6522         TCGA-D7-6524 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-D7-6525         TCGA-D7-6526         TCGA-D7-6527 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-D7-6528         TCGA-D7-6815         TCGA-D7-6817 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-D7-6818         TCGA-D7-6820         TCGA-D7-6822 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-EQ-5647         TCGA-EQ-8122         TCGA-F1-6177 
      "10Q GAIN CNV" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-F1-6874         TCGA-F1-6875         TCGA-FP-7735 
"10Q GAIN WILD-TYPE"       "10Q GAIN CNV"       "10Q GAIN CNV" 
        TCGA-FP-7829         TCGA-FP-7916         TCGA-FP-7998 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-FP-8099         TCGA-FP-8209         TCGA-FP-8210 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-FP-8631         TCGA-HJ-7597         TCGA-IN-7806 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-IN-7808         TCGA-IP-7968 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-B7-5816         TCGA-B7-5818         TCGA-BR-6452 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-BR-6455         TCGA-BR-6457         TCGA-BR-6458 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-BR-6563         TCGA-BR-6564         TCGA-BR-6565 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-BR-6566         TCGA-BR-6705         TCGA-BR-6706 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-BR-6707         TCGA-BR-6709         TCGA-BR-6710 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-BR-6801         TCGA-BR-6802         TCGA-BR-6803 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-BR-6852         TCGA-BR-7196         TCGA-BR-7197 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE"       "10Q GAIN CNV" 
        TCGA-BR-7703         TCGA-BR-7704         TCGA-BR-7707 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-BR-7715         TCGA-BR-7716         TCGA-BR-7717 
      "10Q GAIN CNV" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-BR-7722         TCGA-BR-7723         TCGA-BR-7851 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-BR-7901         TCGA-BR-7957         TCGA-BR-7958 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-BR-7959         TCGA-BR-8059         TCGA-BR-8060 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-BR-8077         TCGA-BR-8078         TCGA-BR-8080 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-BR-8081         TCGA-BR-8284         TCGA-BR-8285 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-BR-8286         TCGA-BR-8289         TCGA-BR-8291 
"10Q GAIN WILD-TYPE"       "10Q GAIN CNV" "10Q GAIN WILD-TYPE" 
        TCGA-BR-8295         TCGA-BR-8296         TCGA-BR-8297 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-BR-8592         TCGA-BR-A4IU         TCGA-BR-A4IV 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-BR-A4IY         TCGA-BR-A4IZ         TCGA-BR-A4J1 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-BR-A4J2         TCGA-BR-A4J4         TCGA-BR-A4J5 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-BR-A4J6         TCGA-BR-A4J8         TCGA-BR-A4J9 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-BR-A4PF         TCGA-BR-A4QI         TCGA-BR-A4QL 
      "10Q GAIN CNV" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-CD-5798         TCGA-CD-5799         TCGA-CD-5800 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-CD-5801         TCGA-CD-5802         TCGA-CD-5803 
      "10Q GAIN CNV" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-CG-4300         TCGA-CG-4301         TCGA-CG-4304 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-CG-4305         TCGA-CG-4306         TCGA-CG-4436 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-CG-4437         TCGA-CG-4438         TCGA-CG-4440 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-CG-4441         TCGA-CG-4443         TCGA-CG-4444 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE"       "10Q GAIN CNV" 
        TCGA-CG-4449         TCGA-CG-4455         TCGA-CG-4460 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE"       "10Q GAIN CNV" 
        TCGA-CG-4462         TCGA-CG-4465         TCGA-CG-4466 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-CG-4469         TCGA-CG-4472         TCGA-CG-4474 
"10Q GAIN WILD-TYPE"       "10Q GAIN CNV" "10Q GAIN WILD-TYPE" 
        TCGA-CG-4477         TCGA-CG-5716         TCGA-CG-5717 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-CG-5718         TCGA-CG-5719         TCGA-CG-5720 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-CG-5721         TCGA-CG-5722         TCGA-CG-5723 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-CG-5724         TCGA-CG-5725         TCGA-CG-5726 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-CG-5727         TCGA-CG-5728         TCGA-CG-5730 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-CG-5732         TCGA-CG-5733         TCGA-CG-5734 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-D7-5577         TCGA-D7-5578         TCGA-D7-5579 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-D7-6518         TCGA-D7-6519         TCGA-D7-6520 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE"       "10Q GAIN CNV" 
        TCGA-D7-6521         TCGA-D7-6522         TCGA-D7-6524 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-D7-6525         TCGA-D7-6526         TCGA-D7-6527 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-D7-6528         TCGA-D7-6815         TCGA-D7-6817 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-D7-6818         TCGA-D7-6820         TCGA-D7-6822 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-EQ-5647         TCGA-EQ-8122         TCGA-F1-6177 
      "10Q GAIN CNV" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-F1-6874         TCGA-F1-6875         TCGA-FP-7735 
"10Q GAIN WILD-TYPE"       "10Q GAIN CNV"       "10Q GAIN CNV" 
        TCGA-FP-7829         TCGA-FP-7916         TCGA-FP-7998 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-FP-8099         TCGA-FP-8209         TCGA-FP-8210 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-FP-8631         TCGA-HJ-7597         TCGA-IN-7806 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-IN-7808         TCGA-IP-7968 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-B7-5816         TCGA-B7-5818         TCGA-BR-6452 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-BR-6455         TCGA-BR-6457         TCGA-BR-6458 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-BR-6563         TCGA-BR-6564         TCGA-BR-6565 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-BR-6566         TCGA-BR-6705         TCGA-BR-6706 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-BR-6707         TCGA-BR-6709         TCGA-BR-6710 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-BR-6801         TCGA-BR-6802         TCGA-BR-6803 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-BR-6852         TCGA-BR-7196         TCGA-BR-7197 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE"       "10Q GAIN CNV" 
        TCGA-BR-7703         TCGA-BR-7704         TCGA-BR-7707 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-BR-7715         TCGA-BR-7716         TCGA-BR-7717 
      "10Q GAIN CNV" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-BR-7722         TCGA-BR-7723         TCGA-BR-7851 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-BR-7901         TCGA-BR-7957         TCGA-BR-7958 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-BR-7959         TCGA-BR-8059         TCGA-BR-8060 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-BR-8077         TCGA-BR-8078         TCGA-BR-8080 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-BR-8081         TCGA-BR-8284         TCGA-BR-8285 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-BR-8286         TCGA-BR-8289         TCGA-BR-8291 
"10Q GAIN WILD-TYPE"       "10Q GAIN CNV" "10Q GAIN WILD-TYPE" 
        TCGA-BR-8295         TCGA-BR-8296         TCGA-BR-8297 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-BR-8592         TCGA-BR-A4IU         TCGA-BR-A4IV 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-BR-A4IY         TCGA-BR-A4IZ         TCGA-BR-A4J1 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-BR-A4J2         TCGA-BR-A4J4         TCGA-BR-A4J5 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-BR-A4J6         TCGA-BR-A4J8         TCGA-BR-A4J9 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-BR-A4PF         TCGA-BR-A4QI         TCGA-BR-A4QL 
      "10Q GAIN CNV" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-CD-5798         TCGA-CD-5799         TCGA-CD-5800 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-CD-5801         TCGA-CD-5802         TCGA-CD-5803 
      "10Q GAIN CNV" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-CG-4300         TCGA-CG-4301         TCGA-CG-4304 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-CG-4305         TCGA-CG-4306         TCGA-CG-4436 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-CG-4437         TCGA-CG-4438         TCGA-CG-4440 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-CG-4441         TCGA-CG-4443         TCGA-CG-4444 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE"       "10Q GAIN CNV" 
        TCGA-CG-4449         TCGA-CG-4455         TCGA-CG-4460 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE"       "10Q GAIN CNV" 
        TCGA-CG-4462         TCGA-CG-4465         TCGA-CG-4466 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-CG-4469         TCGA-CG-4472         TCGA-CG-4474 
"10Q GAIN WILD-TYPE"       "10Q GAIN CNV" "10Q GAIN WILD-TYPE" 
        TCGA-CG-4477         TCGA-CG-5716         TCGA-CG-5717 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-CG-5718         TCGA-CG-5719         TCGA-CG-5720 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-CG-5721         TCGA-CG-5722         TCGA-CG-5723 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-CG-5724         TCGA-CG-5725         TCGA-CG-5726 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-CG-5727         TCGA-CG-5728         TCGA-CG-5730 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-CG-5732         TCGA-CG-5733         TCGA-CG-5734 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-D7-5577         TCGA-D7-5578         TCGA-D7-5579 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-D7-6518         TCGA-D7-6519         TCGA-D7-6520 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE"       "10Q GAIN CNV" 
        TCGA-D7-6521         TCGA-D7-6522         TCGA-D7-6524 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-D7-6525         TCGA-D7-6526         TCGA-D7-6527 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-D7-6528         TCGA-D7-6815         TCGA-D7-6817 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-D7-6818         TCGA-D7-6820         TCGA-D7-6822 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-EQ-5647         TCGA-EQ-8122         TCGA-F1-6177 
      "10Q GAIN CNV" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-F1-6874         TCGA-F1-6875         TCGA-FP-7735 
"10Q GAIN WILD-TYPE"       "10Q GAIN CNV"       "10Q GAIN CNV" 
        TCGA-FP-7829         TCGA-FP-7916         TCGA-FP-7998 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-FP-8099         TCGA-FP-8209         TCGA-FP-8210 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-FP-8631         TCGA-HJ-7597         TCGA-IN-7806 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-IN-7808         TCGA-IP-7968 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
[1] "hr=" "1.3"
D19V2, continuous
D19V3, binary
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  10Q GAIN CNV          5   10
  10Q GAIN WILD-TYPE   67   98
        clus
vv       10Q GAIN CNV 10Q GAIN WILD-TYPE
  FEMALE            5                 67
  MALE             10                 98
                    vv
clus                 STOMACH  ADENOCARCINOMA  DIFFUSE TYPE
  10Q GAIN CNV                                           0
  10Q GAIN WILD-TYPE                                    10
                    vv
clus                 STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  10Q GAIN CNV                                                            1
  10Q GAIN WILD-TYPE                                                     15
                    vv
clus                 STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  10Q GAIN CNV                                                                       1
  10Q GAIN WILD-TYPE                                                                 7
                    vv
clus                 STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE
  10Q GAIN CNV                                                              0
  10Q GAIN WILD-TYPE                                                        3
                    vv
clus                 STOMACH ADENOCARCINOMA  SIGNET RING TYPE
  10Q GAIN CNV                                              0
  10Q GAIN WILD-TYPE                                        1
                    vv
clus                 STOMACH ADENOCARCINOMA - DIFFUSE TYPE
  10Q GAIN CNV                                           0
  10Q GAIN WILD-TYPE                                    16
                    vv
clus                 STOMACH ADENOCARCINOMA - NOT OTHERWISE SPECIFIED (NOS)
  10Q GAIN CNV                                                            9
  10Q GAIN WILD-TYPE                                                     64
                    vv
clus                 STOMACH INTESTINAL ADENOCARCINOMA - MUCINOUS TYPE
  10Q GAIN CNV                                                       0
  10Q GAIN WILD-TYPE                                                 7
                    vv
clus                 STOMACH INTESTINAL ADENOCARCINOMA - PAPILLARY TYPE
  10Q GAIN CNV                                                        0
  10Q GAIN WILD-TYPE                                                  3
                    vv
clus                 STOMACH INTESTINAL ADENOCARCINOMA - TUBULAR TYPE
  10Q GAIN CNV                                                      1
  10Q GAIN WILD-TYPE                                                9
                    vv
clus                 STOMACH INTESTINAL ADENOCARCINOMA - TYPE NOT OTHERWISE SPECIFIED (NOS)
  10Q GAIN CNV                                                                            1
  10Q GAIN WILD-TYPE                                                                     27
D19V4, multiclass
                    vv
clus                 T1 T2 T3 T4
  10Q GAIN CNV        0  4  5  4
  10Q GAIN WILD-TYPE  6 48 51 14
D19V5, multiclass
    clus
vv   10Q GAIN CNV 10Q GAIN WILD-TYPE
  T1            0                  6
  T2            4                 48
  T3            5                 51
  T4            4                 14
                    vv
clus                 N0 N1 N2 N3
  10Q GAIN CNV        4  5  3  1
  10Q GAIN WILD-TYPE 40 44 20 14
D19V6, multiclass
    clus
vv   10Q GAIN CNV 10Q GAIN WILD-TYPE
  N0            4                 40
  N1            5                 44
  N2            3                 20
  N3            1                 14
                    vv
clus                  M0  M1  MX
  10Q GAIN CNV        10   2   1
  10Q GAIN WILD-TYPE 108  14   7
D19V7, multiclass
    clus
vv   10Q GAIN CNV 10Q GAIN WILD-TYPE
  M0           10                108
  M1            2                 14
  MX            1                  7
                    vv
clus                  I II III IV
  10Q GAIN CNV        2  3   4  4
  10Q GAIN WILD-TYPE 22 34  35 22
D19V8, multiclass
     clus
vv    10Q GAIN CNV 10Q GAIN WILD-TYPE
  I              2                 22
  II             3                 34
  III            4                 35
  IV             4                 22
D19V9, binary
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  10Q GAIN CNV          0   15
  10Q GAIN WILD-TYPE    5  160
     clus
vv    10Q GAIN CNV 10Q GAIN WILD-TYPE
  NO             0                  5
  YES           15                160
                    vv
clus                  R0  R1  R2  RX
  10Q GAIN CNV        10   0   2   2
  10Q GAIN WILD-TYPE 115   7  10  23
D19V10, multiclass
    clus
vv   10Q GAIN CNV 10Q GAIN WILD-TYPE
  R0           10                115
  R1            0                  7
  R2            2                 10
  RX            2                 23
D19V11, continuous

Clustering(20) Variable = 11p gain
D20V1, survival
                    sevent
clus2                  0   1
  11P GAIN CNV         5   0
  11P GAIN WILD-TYPE 119  19
      11P GAIN CNV 11P GAIN WILD-TYPE 
                 5                138 
      11P GAIN CNV 11P GAIN WILD-TYPE 
                 0                 19 
$`11P GAIN CNV`
TCGA-BR-6455 TCGA-BR-A4IY TCGA-CG-4300 TCGA-EQ-8122 TCGA-FP-8099 
        1.41         0.39        20.02         7.79         1.02 

$`11P GAIN WILD-TYPE`
TCGA-B7-5816 TCGA-B7-5818 TCGA-BR-6452 TCGA-BR-6457 TCGA-BR-6458 TCGA-BR-6563 
        5.62         0.10         0.95         1.35         1.35         0.85 
TCGA-BR-6564 TCGA-BR-6565 TCGA-BR-6566 TCGA-BR-6705 TCGA-BR-6706 TCGA-BR-6707 
        0.82         0.62         0.62         1.71         2.17         0.99 
TCGA-BR-6709 TCGA-BR-6710 TCGA-BR-6801 TCGA-BR-6802 TCGA-BR-6803 TCGA-BR-6852 
        1.22         0.66         1.12         0.76         0.66         0.26 
TCGA-BR-7196 TCGA-BR-7197 TCGA-BR-7703 TCGA-BR-7704 TCGA-BR-7707 TCGA-BR-7715 
        1.22         1.48         0.46         1.25         0.13         1.05 
TCGA-BR-7716 TCGA-BR-7717 TCGA-BR-7722 TCGA-BR-7723 TCGA-BR-7851 TCGA-BR-7901 
        0.82         0.69         0.16         4.54         0.99         0.95 
TCGA-BR-7957 TCGA-BR-7958 TCGA-BR-7959 TCGA-BR-8059 TCGA-BR-8060 TCGA-BR-8077 
        0.69         0.16         1.08         0.82         1.32         0.69 
TCGA-BR-8078 TCGA-BR-8080 TCGA-BR-8081 TCGA-BR-8284 TCGA-BR-8285 TCGA-BR-8286 
        0.95         0.49         0.46         0.72         0.26         0.43 
TCGA-BR-8289 TCGA-BR-8291 TCGA-BR-8295 TCGA-BR-8296 TCGA-BR-8297 TCGA-BR-8592 
        0.26         1.18         1.55         1.48         0.76         0.20 
TCGA-BR-A4IU TCGA-BR-A4IV TCGA-BR-A4IZ TCGA-BR-A4J1 TCGA-BR-A4J2 TCGA-BR-A4J4 
        0.59         0.92         0.79         0.72         0.79         0.53 
TCGA-BR-A4J5 TCGA-BR-A4J6 TCGA-BR-A4J8 TCGA-BR-A4J9 TCGA-BR-A4PF TCGA-BR-A4QI 
        0.43         0.13         0.23         0.10         0.72         0.49 
TCGA-BR-A4QL TCGA-CD-5798 TCGA-CD-5799 TCGA-CD-5800 TCGA-CD-5801 TCGA-CD-5802 
        2.24         0.82         0.69         0.36         0.49         0.30 
TCGA-CD-5803 TCGA-CG-4301 TCGA-CG-4304 TCGA-CG-4305 TCGA-CG-4306 TCGA-CG-4436 
        0.07         3.02        27.02        15.95         1.02        52.96 
TCGA-CG-4437 TCGA-CG-4438 TCGA-CG-4440 TCGA-CG-4441 TCGA-CG-4443 TCGA-CG-4444 
        8.05        54.05         4.01        14.01        29.98        47.05 
TCGA-CG-4449 TCGA-CG-4455 TCGA-CG-4460 TCGA-CG-4462 TCGA-CG-4465 TCGA-CG-4466 
       19.07        12.03        21.99         1.02         8.98        18.94 
TCGA-CG-4469 TCGA-CG-4472 TCGA-CG-4474 TCGA-CG-4477 TCGA-CG-5716 TCGA-CG-5717 
        7.07        12.00         1.02         1.02         1.02         6.94 
TCGA-CG-5718 TCGA-CG-5719 TCGA-CG-5720 TCGA-CG-5721 TCGA-CG-5722 TCGA-CG-5723 
        1.02         1.02         0.99         5.98         0.95        70.06 
TCGA-CG-5724 TCGA-CG-5725 TCGA-CG-5726 TCGA-CG-5727 TCGA-CG-5728 TCGA-CG-5730 
       12.03        15.02        28.96        31.04        65.10         4.01 
TCGA-CG-5732 TCGA-CG-5733 TCGA-CG-5734 TCGA-D7-5577 TCGA-D7-5578 TCGA-D7-5579 
       55.04        21.07         7.99         8.65         3.58         4.54 
TCGA-D7-6518 TCGA-D7-6519 TCGA-D7-6520 TCGA-D7-6521 TCGA-D7-6522 TCGA-D7-6524 
        9.80        15.65         9.63         8.19         6.90         0.69 
TCGA-D7-6525 TCGA-D7-6526 TCGA-D7-6527 TCGA-D7-6528 TCGA-D7-6815 TCGA-D7-6817 
        5.95         6.61         4.14         1.68         3.65         4.70 
TCGA-D7-6818 TCGA-D7-6820 TCGA-D7-6822 TCGA-EQ-5647 TCGA-F1-6177 TCGA-F1-6874 
        4.04         2.93         4.27         0.62         6.54         2.01 
TCGA-F1-6875 TCGA-FP-7735 TCGA-FP-7829 TCGA-FP-7916 TCGA-FP-7998 TCGA-FP-8209 
       72.23         0.39         0.20         3.02         3.58        59.05 
TCGA-FP-8210 TCGA-FP-8631 TCGA-HJ-7597 TCGA-IN-7806 TCGA-IN-7808 TCGA-IP-7968 
        5.03         0.56        26.43         6.87         3.55         2.53 

      11P GAIN CNV 11P GAIN WILD-TYPE 
              0.39               0.07 
      11P GAIN CNV 11P GAIN WILD-TYPE 
             20.02              72.23 
      11P GAIN CNV 11P GAIN WILD-TYPE 
             1.410              1.235 
[1] "0.4 - 20.0 (1.4)" "0.1 - 72.2 (1.2)"
        TCGA-B7-5816         TCGA-B7-5818         TCGA-BR-6452 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-BR-6455         TCGA-BR-6457         TCGA-BR-6458 
      "11P GAIN CNV" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-BR-6563         TCGA-BR-6564         TCGA-BR-6565 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-BR-6566         TCGA-BR-6705         TCGA-BR-6706 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-BR-6707         TCGA-BR-6709         TCGA-BR-6710 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-BR-6801         TCGA-BR-6802         TCGA-BR-6803 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-BR-6852         TCGA-BR-7196         TCGA-BR-7197 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-BR-7703         TCGA-BR-7704         TCGA-BR-7707 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-BR-7715         TCGA-BR-7716         TCGA-BR-7717 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-BR-7722         TCGA-BR-7723         TCGA-BR-7851 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-BR-7901         TCGA-BR-7957         TCGA-BR-7958 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-BR-7959         TCGA-BR-8059         TCGA-BR-8060 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-BR-8077         TCGA-BR-8078         TCGA-BR-8080 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-BR-8081         TCGA-BR-8284         TCGA-BR-8285 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-BR-8286         TCGA-BR-8289         TCGA-BR-8291 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-BR-8295         TCGA-BR-8296         TCGA-BR-8297 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-BR-8592         TCGA-BR-A4IU         TCGA-BR-A4IV 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-BR-A4IY         TCGA-BR-A4IZ         TCGA-BR-A4J1 
      "11P GAIN CNV" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-BR-A4J2         TCGA-BR-A4J4         TCGA-BR-A4J5 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-BR-A4J6         TCGA-BR-A4J8         TCGA-BR-A4J9 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-BR-A4PF         TCGA-BR-A4QI         TCGA-BR-A4QL 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-CD-5798         TCGA-CD-5799         TCGA-CD-5800 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-CD-5801         TCGA-CD-5802         TCGA-CD-5803 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-CG-4300         TCGA-CG-4301         TCGA-CG-4304 
      "11P GAIN CNV" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-CG-4305         TCGA-CG-4306         TCGA-CG-4436 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-CG-4437         TCGA-CG-4438         TCGA-CG-4440 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-CG-4441         TCGA-CG-4443         TCGA-CG-4444 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-CG-4449         TCGA-CG-4455         TCGA-CG-4460 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-CG-4462         TCGA-CG-4465         TCGA-CG-4466 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-CG-4469         TCGA-CG-4472         TCGA-CG-4474 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-CG-4477         TCGA-CG-5716         TCGA-CG-5717 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-CG-5718         TCGA-CG-5719         TCGA-CG-5720 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-CG-5721         TCGA-CG-5722         TCGA-CG-5723 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-CG-5724         TCGA-CG-5725         TCGA-CG-5726 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-CG-5727         TCGA-CG-5728         TCGA-CG-5730 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-CG-5732         TCGA-CG-5733         TCGA-CG-5734 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-D7-5577         TCGA-D7-5578         TCGA-D7-5579 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-D7-6518         TCGA-D7-6519         TCGA-D7-6520 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-D7-6521         TCGA-D7-6522         TCGA-D7-6524 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-D7-6525         TCGA-D7-6526         TCGA-D7-6527 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-D7-6528         TCGA-D7-6815         TCGA-D7-6817 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-D7-6818         TCGA-D7-6820         TCGA-D7-6822 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-EQ-5647         TCGA-EQ-8122         TCGA-F1-6177 
"11P GAIN WILD-TYPE"       "11P GAIN CNV" "11P GAIN WILD-TYPE" 
        TCGA-F1-6874         TCGA-F1-6875         TCGA-FP-7735 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-FP-7829         TCGA-FP-7916         TCGA-FP-7998 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-FP-8099         TCGA-FP-8209         TCGA-FP-8210 
      "11P GAIN CNV" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-FP-8631         TCGA-HJ-7597         TCGA-IN-7806 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-IN-7808         TCGA-IP-7968 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-B7-5816         TCGA-B7-5818         TCGA-BR-6452 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-BR-6455         TCGA-BR-6457         TCGA-BR-6458 
      "11P GAIN CNV" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-BR-6563         TCGA-BR-6564         TCGA-BR-6565 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-BR-6566         TCGA-BR-6705         TCGA-BR-6706 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-BR-6707         TCGA-BR-6709         TCGA-BR-6710 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-BR-6801         TCGA-BR-6802         TCGA-BR-6803 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-BR-6852         TCGA-BR-7196         TCGA-BR-7197 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-BR-7703         TCGA-BR-7704         TCGA-BR-7707 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-BR-7715         TCGA-BR-7716         TCGA-BR-7717 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-BR-7722         TCGA-BR-7723         TCGA-BR-7851 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-BR-7901         TCGA-BR-7957         TCGA-BR-7958 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-BR-7959         TCGA-BR-8059         TCGA-BR-8060 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-BR-8077         TCGA-BR-8078         TCGA-BR-8080 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-BR-8081         TCGA-BR-8284         TCGA-BR-8285 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-BR-8286         TCGA-BR-8289         TCGA-BR-8291 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-BR-8295         TCGA-BR-8296         TCGA-BR-8297 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-BR-8592         TCGA-BR-A4IU         TCGA-BR-A4IV 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-BR-A4IY         TCGA-BR-A4IZ         TCGA-BR-A4J1 
      "11P GAIN CNV" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-BR-A4J2         TCGA-BR-A4J4         TCGA-BR-A4J5 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-BR-A4J6         TCGA-BR-A4J8         TCGA-BR-A4J9 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-BR-A4PF         TCGA-BR-A4QI         TCGA-BR-A4QL 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-CD-5798         TCGA-CD-5799         TCGA-CD-5800 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-CD-5801         TCGA-CD-5802         TCGA-CD-5803 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-CG-4300         TCGA-CG-4301         TCGA-CG-4304 
      "11P GAIN CNV" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-CG-4305         TCGA-CG-4306         TCGA-CG-4436 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-CG-4437         TCGA-CG-4438         TCGA-CG-4440 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-CG-4441         TCGA-CG-4443         TCGA-CG-4444 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-CG-4449         TCGA-CG-4455         TCGA-CG-4460 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-CG-4462         TCGA-CG-4465         TCGA-CG-4466 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-CG-4469         TCGA-CG-4472         TCGA-CG-4474 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-CG-4477         TCGA-CG-5716         TCGA-CG-5717 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-CG-5718         TCGA-CG-5719         TCGA-CG-5720 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-CG-5721         TCGA-CG-5722         TCGA-CG-5723 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-CG-5724         TCGA-CG-5725         TCGA-CG-5726 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-CG-5727         TCGA-CG-5728         TCGA-CG-5730 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-CG-5732         TCGA-CG-5733         TCGA-CG-5734 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-D7-5577         TCGA-D7-5578         TCGA-D7-5579 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-D7-6518         TCGA-D7-6519         TCGA-D7-6520 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-D7-6521         TCGA-D7-6522         TCGA-D7-6524 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-D7-6525         TCGA-D7-6526         TCGA-D7-6527 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-D7-6528         TCGA-D7-6815         TCGA-D7-6817 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-D7-6818         TCGA-D7-6820         TCGA-D7-6822 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-EQ-5647         TCGA-EQ-8122         TCGA-F1-6177 
"11P GAIN WILD-TYPE"       "11P GAIN CNV" "11P GAIN WILD-TYPE" 
        TCGA-F1-6874         TCGA-F1-6875         TCGA-FP-7735 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-FP-7829         TCGA-FP-7916         TCGA-FP-7998 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-FP-8099         TCGA-FP-8209         TCGA-FP-8210 
      "11P GAIN CNV" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-FP-8631         TCGA-HJ-7597         TCGA-IN-7806 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-IN-7808         TCGA-IP-7968 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-B7-5816         TCGA-B7-5818         TCGA-BR-6452 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-BR-6455         TCGA-BR-6457         TCGA-BR-6458 
      "11P GAIN CNV" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-BR-6563         TCGA-BR-6564         TCGA-BR-6565 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-BR-6566         TCGA-BR-6705         TCGA-BR-6706 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-BR-6707         TCGA-BR-6709         TCGA-BR-6710 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-BR-6801         TCGA-BR-6802         TCGA-BR-6803 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-BR-6852         TCGA-BR-7196         TCGA-BR-7197 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-BR-7703         TCGA-BR-7704         TCGA-BR-7707 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-BR-7715         TCGA-BR-7716         TCGA-BR-7717 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-BR-7722         TCGA-BR-7723         TCGA-BR-7851 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-BR-7901         TCGA-BR-7957         TCGA-BR-7958 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-BR-7959         TCGA-BR-8059         TCGA-BR-8060 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-BR-8077         TCGA-BR-8078         TCGA-BR-8080 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-BR-8081         TCGA-BR-8284         TCGA-BR-8285 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-BR-8286         TCGA-BR-8289         TCGA-BR-8291 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-BR-8295         TCGA-BR-8296         TCGA-BR-8297 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-BR-8592         TCGA-BR-A4IU         TCGA-BR-A4IV 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-BR-A4IY         TCGA-BR-A4IZ         TCGA-BR-A4J1 
      "11P GAIN CNV" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-BR-A4J2         TCGA-BR-A4J4         TCGA-BR-A4J5 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-BR-A4J6         TCGA-BR-A4J8         TCGA-BR-A4J9 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-BR-A4PF         TCGA-BR-A4QI         TCGA-BR-A4QL 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-CD-5798         TCGA-CD-5799         TCGA-CD-5800 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-CD-5801         TCGA-CD-5802         TCGA-CD-5803 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-CG-4300         TCGA-CG-4301         TCGA-CG-4304 
      "11P GAIN CNV" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-CG-4305         TCGA-CG-4306         TCGA-CG-4436 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-CG-4437         TCGA-CG-4438         TCGA-CG-4440 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-CG-4441         TCGA-CG-4443         TCGA-CG-4444 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-CG-4449         TCGA-CG-4455         TCGA-CG-4460 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-CG-4462         TCGA-CG-4465         TCGA-CG-4466 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-CG-4469         TCGA-CG-4472         TCGA-CG-4474 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-CG-4477         TCGA-CG-5716         TCGA-CG-5717 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-CG-5718         TCGA-CG-5719         TCGA-CG-5720 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-CG-5721         TCGA-CG-5722         TCGA-CG-5723 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-CG-5724         TCGA-CG-5725         TCGA-CG-5726 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-CG-5727         TCGA-CG-5728         TCGA-CG-5730 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-CG-5732         TCGA-CG-5733         TCGA-CG-5734 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-D7-5577         TCGA-D7-5578         TCGA-D7-5579 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-D7-6518         TCGA-D7-6519         TCGA-D7-6520 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-D7-6521         TCGA-D7-6522         TCGA-D7-6524 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-D7-6525         TCGA-D7-6526         TCGA-D7-6527 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-D7-6528         TCGA-D7-6815         TCGA-D7-6817 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-D7-6818         TCGA-D7-6820         TCGA-D7-6822 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-EQ-5647         TCGA-EQ-8122         TCGA-F1-6177 
"11P GAIN WILD-TYPE"       "11P GAIN CNV" "11P GAIN WILD-TYPE" 
        TCGA-F1-6874         TCGA-F1-6875         TCGA-FP-7735 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-FP-7829         TCGA-FP-7916         TCGA-FP-7998 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-FP-8099         TCGA-FP-8209         TCGA-FP-8210 
      "11P GAIN CNV" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-FP-8631         TCGA-HJ-7597         TCGA-IN-7806 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-IN-7808         TCGA-IP-7968 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
[1] "hr="     "2.6e+07"
D20V2, continuous
D20V3, binary
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  11P GAIN CNV          2    5
  11P GAIN WILD-TYPE   70  103
        clus
vv       11P GAIN CNV 11P GAIN WILD-TYPE
  FEMALE            2                 70
  MALE              5                103
                    vv
clus                 STOMACH  ADENOCARCINOMA  DIFFUSE TYPE
  11P GAIN CNV                                           0
  11P GAIN WILD-TYPE                                    10
                    vv
clus                 STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  11P GAIN CNV                                                            2
  11P GAIN WILD-TYPE                                                     14
                    vv
clus                 STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  11P GAIN CNV                                                                       1
  11P GAIN WILD-TYPE                                                                 7
                    vv
clus                 STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE
  11P GAIN CNV                                                              0
  11P GAIN WILD-TYPE                                                        3
                    vv
clus                 STOMACH ADENOCARCINOMA  SIGNET RING TYPE
  11P GAIN CNV                                              0
  11P GAIN WILD-TYPE                                        1
                    vv
clus                 STOMACH ADENOCARCINOMA - DIFFUSE TYPE
  11P GAIN CNV                                           0
  11P GAIN WILD-TYPE                                    16
                    vv
clus                 STOMACH ADENOCARCINOMA - NOT OTHERWISE SPECIFIED (NOS)
  11P GAIN CNV                                                            4
  11P GAIN WILD-TYPE                                                     69
                    vv
clus                 STOMACH INTESTINAL ADENOCARCINOMA - MUCINOUS TYPE
  11P GAIN CNV                                                       0
  11P GAIN WILD-TYPE                                                 7
                    vv
clus                 STOMACH INTESTINAL ADENOCARCINOMA - PAPILLARY TYPE
  11P GAIN CNV                                                        0
  11P GAIN WILD-TYPE                                                  3
                    vv
clus                 STOMACH INTESTINAL ADENOCARCINOMA - TUBULAR TYPE
  11P GAIN CNV                                                      0
  11P GAIN WILD-TYPE                                               10
                    vv
clus                 STOMACH INTESTINAL ADENOCARCINOMA - TYPE NOT OTHERWISE SPECIFIED (NOS)
  11P GAIN CNV                                                                            0
  11P GAIN WILD-TYPE                                                                     28
D20V4, multiclass
                    vv
clus                 T1 T2 T3 T4
  11P GAIN CNV        0  0  3  1
  11P GAIN WILD-TYPE  6 52 53 17
D20V5, multiclass
    clus
vv   11P GAIN CNV 11P GAIN WILD-TYPE
  T1            0                  6
  T2            0                 52
  T3            3                 53
  T4            1                 17
                    vv
clus                 N0 N1 N2 N3
  11P GAIN CNV        0  2  2  0
  11P GAIN WILD-TYPE 44 47 21 15
D20V6, multiclass
    clus
vv   11P GAIN CNV 11P GAIN WILD-TYPE
  N0            0                 44
  N1            2                 47
  N2            2                 21
  N3            0                 15
                    vv
clus                  M0  M1  MX
  11P GAIN CNV         4   0   0
  11P GAIN WILD-TYPE 114  16   8
D20V7, multiclass
    clus
vv   11P GAIN CNV 11P GAIN WILD-TYPE
  M0            4                114
  M1            0                 16
  MX            0                  8
                    vv
clus                  I II III IV
  11P GAIN CNV        0  0   3  1
  11P GAIN WILD-TYPE 24 37  36 25
D20V8, multiclass
     clus
vv    11P GAIN CNV 11P GAIN WILD-TYPE
  I              0                 24
  II             0                 37
  III            3                 36
  IV             1                 25
D20V9, binary
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  11P GAIN CNV          0    7
  11P GAIN WILD-TYPE    5  168
     clus
vv    11P GAIN CNV 11P GAIN WILD-TYPE
  NO             0                  5
  YES            7                168
                    vv
clus                  R0  R1  R2  RX
  11P GAIN CNV         4   1   0   1
  11P GAIN WILD-TYPE 121   6  12  24
D20V10, multiclass
    clus
vv   11P GAIN CNV 11P GAIN WILD-TYPE
  R0            4                121
  R1            1                  6
  R2            0                 12
  RX            1                 24
D20V11, continuous

Clustering(21) Variable = 11q gain
D21V1, survival
                    sevent
clus2                  0   1
  11Q GAIN CNV         9   1
  11Q GAIN WILD-TYPE 115  18
      11Q GAIN CNV 11Q GAIN WILD-TYPE 
                10                133 
      11Q GAIN CNV 11Q GAIN WILD-TYPE 
                 1                 18 
$`11Q GAIN CNV`
TCGA-BR-6455 TCGA-BR-7704 TCGA-BR-8077 TCGA-BR-A4IY TCGA-CG-4300 TCGA-CG-4472 
        1.41         1.25         0.69         0.39        20.02        12.00 
TCGA-D7-6528 TCGA-EQ-8122 TCGA-F1-6875 TCGA-FP-8099 
        1.68         7.79        72.23         1.02 

$`11Q GAIN WILD-TYPE`
TCGA-B7-5816 TCGA-B7-5818 TCGA-BR-6452 TCGA-BR-6457 TCGA-BR-6458 TCGA-BR-6563 
        5.62         0.10         0.95         1.35         1.35         0.85 
TCGA-BR-6564 TCGA-BR-6565 TCGA-BR-6566 TCGA-BR-6705 TCGA-BR-6706 TCGA-BR-6707 
        0.82         0.62         0.62         1.71         2.17         0.99 
TCGA-BR-6709 TCGA-BR-6710 TCGA-BR-6801 TCGA-BR-6802 TCGA-BR-6803 TCGA-BR-6852 
        1.22         0.66         1.12         0.76         0.66         0.26 
TCGA-BR-7196 TCGA-BR-7197 TCGA-BR-7703 TCGA-BR-7707 TCGA-BR-7715 TCGA-BR-7716 
        1.22         1.48         0.46         0.13         1.05         0.82 
TCGA-BR-7717 TCGA-BR-7722 TCGA-BR-7723 TCGA-BR-7851 TCGA-BR-7901 TCGA-BR-7957 
        0.69         0.16         4.54         0.99         0.95         0.69 
TCGA-BR-7958 TCGA-BR-7959 TCGA-BR-8059 TCGA-BR-8060 TCGA-BR-8078 TCGA-BR-8080 
        0.16         1.08         0.82         1.32         0.95         0.49 
TCGA-BR-8081 TCGA-BR-8284 TCGA-BR-8285 TCGA-BR-8286 TCGA-BR-8289 TCGA-BR-8291 
        0.46         0.72         0.26         0.43         0.26         1.18 
TCGA-BR-8295 TCGA-BR-8296 TCGA-BR-8297 TCGA-BR-8592 TCGA-BR-A4IU TCGA-BR-A4IV 
        1.55         1.48         0.76         0.20         0.59         0.92 
TCGA-BR-A4IZ TCGA-BR-A4J1 TCGA-BR-A4J2 TCGA-BR-A4J4 TCGA-BR-A4J5 TCGA-BR-A4J6 
        0.79         0.72         0.79         0.53         0.43         0.13 
TCGA-BR-A4J8 TCGA-BR-A4J9 TCGA-BR-A4PF TCGA-BR-A4QI TCGA-BR-A4QL TCGA-CD-5798 
        0.23         0.10         0.72         0.49         2.24         0.82 
TCGA-CD-5799 TCGA-CD-5800 TCGA-CD-5801 TCGA-CD-5802 TCGA-CD-5803 TCGA-CG-4301 
        0.69         0.36         0.49         0.30         0.07         3.02 
TCGA-CG-4304 TCGA-CG-4305 TCGA-CG-4306 TCGA-CG-4436 TCGA-CG-4437 TCGA-CG-4438 
       27.02        15.95         1.02        52.96         8.05        54.05 
TCGA-CG-4440 TCGA-CG-4441 TCGA-CG-4443 TCGA-CG-4444 TCGA-CG-4449 TCGA-CG-4455 
        4.01        14.01        29.98        47.05        19.07        12.03 
TCGA-CG-4460 TCGA-CG-4462 TCGA-CG-4465 TCGA-CG-4466 TCGA-CG-4469 TCGA-CG-4474 
       21.99         1.02         8.98        18.94         7.07         1.02 
TCGA-CG-4477 TCGA-CG-5716 TCGA-CG-5717 TCGA-CG-5718 TCGA-CG-5719 TCGA-CG-5720 
        1.02         1.02         6.94         1.02         1.02         0.99 
TCGA-CG-5721 TCGA-CG-5722 TCGA-CG-5723 TCGA-CG-5724 TCGA-CG-5725 TCGA-CG-5726 
        5.98         0.95        70.06        12.03        15.02        28.96 
TCGA-CG-5727 TCGA-CG-5728 TCGA-CG-5730 TCGA-CG-5732 TCGA-CG-5733 TCGA-CG-5734 
       31.04        65.10         4.01        55.04        21.07         7.99 
TCGA-D7-5577 TCGA-D7-5578 TCGA-D7-5579 TCGA-D7-6518 TCGA-D7-6519 TCGA-D7-6520 
        8.65         3.58         4.54         9.80        15.65         9.63 
TCGA-D7-6521 TCGA-D7-6522 TCGA-D7-6524 TCGA-D7-6525 TCGA-D7-6526 TCGA-D7-6527 
        8.19         6.90         0.69         5.95         6.61         4.14 
TCGA-D7-6815 TCGA-D7-6817 TCGA-D7-6818 TCGA-D7-6820 TCGA-D7-6822 TCGA-EQ-5647 
        3.65         4.70         4.04         2.93         4.27         0.62 
TCGA-F1-6177 TCGA-F1-6874 TCGA-FP-7735 TCGA-FP-7829 TCGA-FP-7916 TCGA-FP-7998 
        6.54         2.01         0.39         0.20         3.02         3.58 
TCGA-FP-8209 TCGA-FP-8210 TCGA-FP-8631 TCGA-HJ-7597 TCGA-IN-7806 TCGA-IN-7808 
       59.05         5.03         0.56        26.43         6.87         3.55 
TCGA-IP-7968 
        2.53 

      11Q GAIN CNV 11Q GAIN WILD-TYPE 
              0.39               0.07 
      11Q GAIN CNV 11Q GAIN WILD-TYPE 
             72.23              70.06 
      11Q GAIN CNV 11Q GAIN WILD-TYPE 
             1.545              1.220 
[1] "0.4 - 72.2 (1.5)" "0.1 - 70.1 (1.2)"
        TCGA-B7-5816         TCGA-B7-5818         TCGA-BR-6452 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-BR-6455         TCGA-BR-6457         TCGA-BR-6458 
      "11Q GAIN CNV" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-BR-6563         TCGA-BR-6564         TCGA-BR-6565 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-BR-6566         TCGA-BR-6705         TCGA-BR-6706 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-BR-6707         TCGA-BR-6709         TCGA-BR-6710 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-BR-6801         TCGA-BR-6802         TCGA-BR-6803 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-BR-6852         TCGA-BR-7196         TCGA-BR-7197 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-BR-7703         TCGA-BR-7704         TCGA-BR-7707 
"11Q GAIN WILD-TYPE"       "11Q GAIN CNV" "11Q GAIN WILD-TYPE" 
        TCGA-BR-7715         TCGA-BR-7716         TCGA-BR-7717 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-BR-7722         TCGA-BR-7723         TCGA-BR-7851 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-BR-7901         TCGA-BR-7957         TCGA-BR-7958 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-BR-7959         TCGA-BR-8059         TCGA-BR-8060 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-BR-8077         TCGA-BR-8078         TCGA-BR-8080 
      "11Q GAIN CNV" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-BR-8081         TCGA-BR-8284         TCGA-BR-8285 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-BR-8286         TCGA-BR-8289         TCGA-BR-8291 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-BR-8295         TCGA-BR-8296         TCGA-BR-8297 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-BR-8592         TCGA-BR-A4IU         TCGA-BR-A4IV 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-BR-A4IY         TCGA-BR-A4IZ         TCGA-BR-A4J1 
      "11Q GAIN CNV" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-BR-A4J2         TCGA-BR-A4J4         TCGA-BR-A4J5 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-BR-A4J6         TCGA-BR-A4J8         TCGA-BR-A4J9 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-BR-A4PF         TCGA-BR-A4QI         TCGA-BR-A4QL 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-CD-5798         TCGA-CD-5799         TCGA-CD-5800 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-CD-5801         TCGA-CD-5802         TCGA-CD-5803 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-CG-4300         TCGA-CG-4301         TCGA-CG-4304 
      "11Q GAIN CNV" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-CG-4305         TCGA-CG-4306         TCGA-CG-4436 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-CG-4437         TCGA-CG-4438         TCGA-CG-4440 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-CG-4441         TCGA-CG-4443         TCGA-CG-4444 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-CG-4449         TCGA-CG-4455         TCGA-CG-4460 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-CG-4462         TCGA-CG-4465         TCGA-CG-4466 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-CG-4469         TCGA-CG-4472         TCGA-CG-4474 
"11Q GAIN WILD-TYPE"       "11Q GAIN CNV" "11Q GAIN WILD-TYPE" 
        TCGA-CG-4477         TCGA-CG-5716         TCGA-CG-5717 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-CG-5718         TCGA-CG-5719         TCGA-CG-5720 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-CG-5721         TCGA-CG-5722         TCGA-CG-5723 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-CG-5724         TCGA-CG-5725         TCGA-CG-5726 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-CG-5727         TCGA-CG-5728         TCGA-CG-5730 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-CG-5732         TCGA-CG-5733         TCGA-CG-5734 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-D7-5577         TCGA-D7-5578         TCGA-D7-5579 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-D7-6518         TCGA-D7-6519         TCGA-D7-6520 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-D7-6521         TCGA-D7-6522         TCGA-D7-6524 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-D7-6525         TCGA-D7-6526         TCGA-D7-6527 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-D7-6528         TCGA-D7-6815         TCGA-D7-6817 
      "11Q GAIN CNV" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-D7-6818         TCGA-D7-6820         TCGA-D7-6822 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-EQ-5647         TCGA-EQ-8122         TCGA-F1-6177 
"11Q GAIN WILD-TYPE"       "11Q GAIN CNV" "11Q GAIN WILD-TYPE" 
        TCGA-F1-6874         TCGA-F1-6875         TCGA-FP-7735 
"11Q GAIN WILD-TYPE"       "11Q GAIN CNV" "11Q GAIN WILD-TYPE" 
        TCGA-FP-7829         TCGA-FP-7916         TCGA-FP-7998 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-FP-8099         TCGA-FP-8209         TCGA-FP-8210 
      "11Q GAIN CNV" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-FP-8631         TCGA-HJ-7597         TCGA-IN-7806 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-IN-7808         TCGA-IP-7968 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-B7-5816         TCGA-B7-5818         TCGA-BR-6452 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-BR-6455         TCGA-BR-6457         TCGA-BR-6458 
      "11Q GAIN CNV" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-BR-6563         TCGA-BR-6564         TCGA-BR-6565 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-BR-6566         TCGA-BR-6705         TCGA-BR-6706 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-BR-6707         TCGA-BR-6709         TCGA-BR-6710 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-BR-6801         TCGA-BR-6802         TCGA-BR-6803 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-BR-6852         TCGA-BR-7196         TCGA-BR-7197 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-BR-7703         TCGA-BR-7704         TCGA-BR-7707 
"11Q GAIN WILD-TYPE"       "11Q GAIN CNV" "11Q GAIN WILD-TYPE" 
        TCGA-BR-7715         TCGA-BR-7716         TCGA-BR-7717 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-BR-7722         TCGA-BR-7723         TCGA-BR-7851 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-BR-7901         TCGA-BR-7957         TCGA-BR-7958 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-BR-7959         TCGA-BR-8059         TCGA-BR-8060 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-BR-8077         TCGA-BR-8078         TCGA-BR-8080 
      "11Q GAIN CNV" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-BR-8081         TCGA-BR-8284         TCGA-BR-8285 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-BR-8286         TCGA-BR-8289         TCGA-BR-8291 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-BR-8295         TCGA-BR-8296         TCGA-BR-8297 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-BR-8592         TCGA-BR-A4IU         TCGA-BR-A4IV 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-BR-A4IY         TCGA-BR-A4IZ         TCGA-BR-A4J1 
      "11Q GAIN CNV" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-BR-A4J2         TCGA-BR-A4J4         TCGA-BR-A4J5 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-BR-A4J6         TCGA-BR-A4J8         TCGA-BR-A4J9 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-BR-A4PF         TCGA-BR-A4QI         TCGA-BR-A4QL 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-CD-5798         TCGA-CD-5799         TCGA-CD-5800 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-CD-5801         TCGA-CD-5802         TCGA-CD-5803 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-CG-4300         TCGA-CG-4301         TCGA-CG-4304 
      "11Q GAIN CNV" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-CG-4305         TCGA-CG-4306         TCGA-CG-4436 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-CG-4437         TCGA-CG-4438         TCGA-CG-4440 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-CG-4441         TCGA-CG-4443         TCGA-CG-4444 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-CG-4449         TCGA-CG-4455         TCGA-CG-4460 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-CG-4462         TCGA-CG-4465         TCGA-CG-4466 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-CG-4469         TCGA-CG-4472         TCGA-CG-4474 
"11Q GAIN WILD-TYPE"       "11Q GAIN CNV" "11Q GAIN WILD-TYPE" 
        TCGA-CG-4477         TCGA-CG-5716         TCGA-CG-5717 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-CG-5718         TCGA-CG-5719         TCGA-CG-5720 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-CG-5721         TCGA-CG-5722         TCGA-CG-5723 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-CG-5724         TCGA-CG-5725         TCGA-CG-5726 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-CG-5727         TCGA-CG-5728         TCGA-CG-5730 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-CG-5732         TCGA-CG-5733         TCGA-CG-5734 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-D7-5577         TCGA-D7-5578         TCGA-D7-5579 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-D7-6518         TCGA-D7-6519         TCGA-D7-6520 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-D7-6521         TCGA-D7-6522         TCGA-D7-6524 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-D7-6525         TCGA-D7-6526         TCGA-D7-6527 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-D7-6528         TCGA-D7-6815         TCGA-D7-6817 
      "11Q GAIN CNV" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-D7-6818         TCGA-D7-6820         TCGA-D7-6822 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-EQ-5647         TCGA-EQ-8122         TCGA-F1-6177 
"11Q GAIN WILD-TYPE"       "11Q GAIN CNV" "11Q GAIN WILD-TYPE" 
        TCGA-F1-6874         TCGA-F1-6875         TCGA-FP-7735 
"11Q GAIN WILD-TYPE"       "11Q GAIN CNV" "11Q GAIN WILD-TYPE" 
        TCGA-FP-7829         TCGA-FP-7916         TCGA-FP-7998 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-FP-8099         TCGA-FP-8209         TCGA-FP-8210 
      "11Q GAIN CNV" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-FP-8631         TCGA-HJ-7597         TCGA-IN-7806 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-IN-7808         TCGA-IP-7968 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-B7-5816         TCGA-B7-5818         TCGA-BR-6452 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-BR-6455         TCGA-BR-6457         TCGA-BR-6458 
      "11Q GAIN CNV" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-BR-6563         TCGA-BR-6564         TCGA-BR-6565 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-BR-6566         TCGA-BR-6705         TCGA-BR-6706 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-BR-6707         TCGA-BR-6709         TCGA-BR-6710 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-BR-6801         TCGA-BR-6802         TCGA-BR-6803 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-BR-6852         TCGA-BR-7196         TCGA-BR-7197 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-BR-7703         TCGA-BR-7704         TCGA-BR-7707 
"11Q GAIN WILD-TYPE"       "11Q GAIN CNV" "11Q GAIN WILD-TYPE" 
        TCGA-BR-7715         TCGA-BR-7716         TCGA-BR-7717 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-BR-7722         TCGA-BR-7723         TCGA-BR-7851 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-BR-7901         TCGA-BR-7957         TCGA-BR-7958 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-BR-7959         TCGA-BR-8059         TCGA-BR-8060 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-BR-8077         TCGA-BR-8078         TCGA-BR-8080 
      "11Q GAIN CNV" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-BR-8081         TCGA-BR-8284         TCGA-BR-8285 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-BR-8286         TCGA-BR-8289         TCGA-BR-8291 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-BR-8295         TCGA-BR-8296         TCGA-BR-8297 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-BR-8592         TCGA-BR-A4IU         TCGA-BR-A4IV 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-BR-A4IY         TCGA-BR-A4IZ         TCGA-BR-A4J1 
      "11Q GAIN CNV" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-BR-A4J2         TCGA-BR-A4J4         TCGA-BR-A4J5 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-BR-A4J6         TCGA-BR-A4J8         TCGA-BR-A4J9 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-BR-A4PF         TCGA-BR-A4QI         TCGA-BR-A4QL 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-CD-5798         TCGA-CD-5799         TCGA-CD-5800 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-CD-5801         TCGA-CD-5802         TCGA-CD-5803 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-CG-4300         TCGA-CG-4301         TCGA-CG-4304 
      "11Q GAIN CNV" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-CG-4305         TCGA-CG-4306         TCGA-CG-4436 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-CG-4437         TCGA-CG-4438         TCGA-CG-4440 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-CG-4441         TCGA-CG-4443         TCGA-CG-4444 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-CG-4449         TCGA-CG-4455         TCGA-CG-4460 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-CG-4462         TCGA-CG-4465         TCGA-CG-4466 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-CG-4469         TCGA-CG-4472         TCGA-CG-4474 
"11Q GAIN WILD-TYPE"       "11Q GAIN CNV" "11Q GAIN WILD-TYPE" 
        TCGA-CG-4477         TCGA-CG-5716         TCGA-CG-5717 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-CG-5718         TCGA-CG-5719         TCGA-CG-5720 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-CG-5721         TCGA-CG-5722         TCGA-CG-5723 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-CG-5724         TCGA-CG-5725         TCGA-CG-5726 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-CG-5727         TCGA-CG-5728         TCGA-CG-5730 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-CG-5732         TCGA-CG-5733         TCGA-CG-5734 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-D7-5577         TCGA-D7-5578         TCGA-D7-5579 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-D7-6518         TCGA-D7-6519         TCGA-D7-6520 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-D7-6521         TCGA-D7-6522         TCGA-D7-6524 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-D7-6525         TCGA-D7-6526         TCGA-D7-6527 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-D7-6528         TCGA-D7-6815         TCGA-D7-6817 
      "11Q GAIN CNV" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-D7-6818         TCGA-D7-6820         TCGA-D7-6822 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-EQ-5647         TCGA-EQ-8122         TCGA-F1-6177 
"11Q GAIN WILD-TYPE"       "11Q GAIN CNV" "11Q GAIN WILD-TYPE" 
        TCGA-F1-6874         TCGA-F1-6875         TCGA-FP-7735 
"11Q GAIN WILD-TYPE"       "11Q GAIN CNV" "11Q GAIN WILD-TYPE" 
        TCGA-FP-7829         TCGA-FP-7916         TCGA-FP-7998 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-FP-8099         TCGA-FP-8209         TCGA-FP-8210 
      "11Q GAIN CNV" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-FP-8631         TCGA-HJ-7597         TCGA-IN-7806 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-IN-7808         TCGA-IP-7968 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
[1] "hr="   "8e+07"
D21V2, continuous
D21V3, binary
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  11Q GAIN CNV          5    7
  11Q GAIN WILD-TYPE   67  101
        clus
vv       11Q GAIN CNV 11Q GAIN WILD-TYPE
  FEMALE            5                 67
  MALE              7                101
                    vv
clus                 STOMACH  ADENOCARCINOMA  DIFFUSE TYPE
  11Q GAIN CNV                                           0
  11Q GAIN WILD-TYPE                                    10
                    vv
clus                 STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  11Q GAIN CNV                                                            2
  11Q GAIN WILD-TYPE                                                     14
                    vv
clus                 STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  11Q GAIN CNV                                                                       2
  11Q GAIN WILD-TYPE                                                                 6
                    vv
clus                 STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE
  11Q GAIN CNV                                                              0
  11Q GAIN WILD-TYPE                                                        3
                    vv
clus                 STOMACH ADENOCARCINOMA  SIGNET RING TYPE
  11Q GAIN CNV                                              0
  11Q GAIN WILD-TYPE                                        1
                    vv
clus                 STOMACH ADENOCARCINOMA - DIFFUSE TYPE
  11Q GAIN CNV                                           0
  11Q GAIN WILD-TYPE                                    16
                    vv
clus                 STOMACH ADENOCARCINOMA - NOT OTHERWISE SPECIFIED (NOS)
  11Q GAIN CNV                                                            5
  11Q GAIN WILD-TYPE                                                     68
                    vv
clus                 STOMACH INTESTINAL ADENOCARCINOMA - MUCINOUS TYPE
  11Q GAIN CNV                                                       0
  11Q GAIN WILD-TYPE                                                 7
                    vv
clus                 STOMACH INTESTINAL ADENOCARCINOMA - PAPILLARY TYPE
  11Q GAIN CNV                                                        0
  11Q GAIN WILD-TYPE                                                  3
                    vv
clus                 STOMACH INTESTINAL ADENOCARCINOMA - TUBULAR TYPE
  11Q GAIN CNV                                                      1
  11Q GAIN WILD-TYPE                                                9
                    vv
clus                 STOMACH INTESTINAL ADENOCARCINOMA - TYPE NOT OTHERWISE SPECIFIED (NOS)
  11Q GAIN CNV                                                                            1
  11Q GAIN WILD-TYPE                                                                     27
D21V4, multiclass
                    vv
clus                 T1 T2 T3 T4
  11Q GAIN CNV        0  2  4  2
  11Q GAIN WILD-TYPE  6 50 52 16
D21V5, multiclass
    clus
vv   11Q GAIN CNV 11Q GAIN WILD-TYPE
  T1            0                  6
  T2            2                 50
  T3            4                 52
  T4            2                 16
                    vv
clus                 N0 N1 N2 N3
  11Q GAIN CNV        3  3  2  0
  11Q GAIN WILD-TYPE 41 46 21 15
D21V6, multiclass
    clus
vv   11Q GAIN CNV 11Q GAIN WILD-TYPE
  N0            3                 41
  N1            3                 46
  N2            2                 21
  N3            0                 15
                    vv
clus                  M0  M1  MX
  11Q GAIN CNV         8   0   0
  11Q GAIN WILD-TYPE 110  16   8
D21V7, multiclass
    clus
vv   11Q GAIN CNV 11Q GAIN WILD-TYPE
  M0            8                110
  M1            0                 16
  MX            0                  8
                    vv
clus                  I II III IV
  11Q GAIN CNV        2  1   3  2
  11Q GAIN WILD-TYPE 22 36  36 24
D21V8, multiclass
     clus
vv    11Q GAIN CNV 11Q GAIN WILD-TYPE
  I              2                 22
  II             1                 36
  III            3                 36
  IV             2                 24
D21V9, binary
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  11Q GAIN CNV          0   12
  11Q GAIN WILD-TYPE    5  163
     clus
vv    11Q GAIN CNV 11Q GAIN WILD-TYPE
  NO             0                  5
  YES           12                163
                    vv
clus                  R0  R1  R2  RX
  11Q GAIN CNV         9   1   0   1
  11Q GAIN WILD-TYPE 116   6  12  24
D21V10, multiclass
    clus
vv   11Q GAIN CNV 11Q GAIN WILD-TYPE
  R0            9                116
  R1            1                  6
  R2            0                 12
  RX            1                 24
D21V11, continuous

Clustering(22) Variable = 12p gain
D22V1, survival
                    sevent
clus2                  0   1
  12P GAIN CNV        14   3
  12P GAIN WILD-TYPE 110  16
      12P GAIN CNV 12P GAIN WILD-TYPE 
                17                126 
      12P GAIN CNV 12P GAIN WILD-TYPE 
                 3                 16 
$`12P GAIN CNV`
TCGA-BR-6709 TCGA-BR-6801 TCGA-BR-7723 TCGA-BR-7959 TCGA-BR-8078 TCGA-BR-8295 
        1.22         1.12         4.54         1.08         0.95         1.55 
TCGA-BR-A4J1 TCGA-BR-A4PF TCGA-CD-5799 TCGA-CG-4460 TCGA-CG-5724 TCGA-CG-5727 
        0.72         0.72         0.69        21.99        12.03        31.04 
TCGA-D7-6820 TCGA-FP-7735 TCGA-FP-7829 TCGA-IN-7808 TCGA-IP-7968 
        2.93         0.39         0.20         3.55         2.53 

$`12P GAIN WILD-TYPE`
TCGA-B7-5816 TCGA-B7-5818 TCGA-BR-6452 TCGA-BR-6455 TCGA-BR-6457 TCGA-BR-6458 
        5.62         0.10         0.95         1.41         1.35         1.35 
TCGA-BR-6563 TCGA-BR-6564 TCGA-BR-6565 TCGA-BR-6566 TCGA-BR-6705 TCGA-BR-6706 
        0.85         0.82         0.62         0.62         1.71         2.17 
TCGA-BR-6707 TCGA-BR-6710 TCGA-BR-6802 TCGA-BR-6803 TCGA-BR-6852 TCGA-BR-7196 
        0.99         0.66         0.76         0.66         0.26         1.22 
TCGA-BR-7197 TCGA-BR-7703 TCGA-BR-7704 TCGA-BR-7707 TCGA-BR-7715 TCGA-BR-7716 
        1.48         0.46         1.25         0.13         1.05         0.82 
TCGA-BR-7717 TCGA-BR-7722 TCGA-BR-7851 TCGA-BR-7901 TCGA-BR-7957 TCGA-BR-7958 
        0.69         0.16         0.99         0.95         0.69         0.16 
TCGA-BR-8059 TCGA-BR-8060 TCGA-BR-8077 TCGA-BR-8080 TCGA-BR-8081 TCGA-BR-8284 
        0.82         1.32         0.69         0.49         0.46         0.72 
TCGA-BR-8285 TCGA-BR-8286 TCGA-BR-8289 TCGA-BR-8291 TCGA-BR-8296 TCGA-BR-8297 
        0.26         0.43         0.26         1.18         1.48         0.76 
TCGA-BR-8592 TCGA-BR-A4IU TCGA-BR-A4IV TCGA-BR-A4IY TCGA-BR-A4IZ TCGA-BR-A4J2 
        0.20         0.59         0.92         0.39         0.79         0.79 
TCGA-BR-A4J4 TCGA-BR-A4J5 TCGA-BR-A4J6 TCGA-BR-A4J8 TCGA-BR-A4J9 TCGA-BR-A4QI 
        0.53         0.43         0.13         0.23         0.10         0.49 
TCGA-BR-A4QL TCGA-CD-5798 TCGA-CD-5800 TCGA-CD-5801 TCGA-CD-5802 TCGA-CD-5803 
        2.24         0.82         0.36         0.49         0.30         0.07 
TCGA-CG-4300 TCGA-CG-4301 TCGA-CG-4304 TCGA-CG-4305 TCGA-CG-4306 TCGA-CG-4436 
       20.02         3.02        27.02        15.95         1.02        52.96 
TCGA-CG-4437 TCGA-CG-4438 TCGA-CG-4440 TCGA-CG-4441 TCGA-CG-4443 TCGA-CG-4444 
        8.05        54.05         4.01        14.01        29.98        47.05 
TCGA-CG-4449 TCGA-CG-4455 TCGA-CG-4462 TCGA-CG-4465 TCGA-CG-4466 TCGA-CG-4469 
       19.07        12.03         1.02         8.98        18.94         7.07 
TCGA-CG-4472 TCGA-CG-4474 TCGA-CG-4477 TCGA-CG-5716 TCGA-CG-5717 TCGA-CG-5718 
       12.00         1.02         1.02         1.02         6.94         1.02 
TCGA-CG-5719 TCGA-CG-5720 TCGA-CG-5721 TCGA-CG-5722 TCGA-CG-5723 TCGA-CG-5725 
        1.02         0.99         5.98         0.95        70.06        15.02 
TCGA-CG-5726 TCGA-CG-5728 TCGA-CG-5730 TCGA-CG-5732 TCGA-CG-5733 TCGA-CG-5734 
       28.96        65.10         4.01        55.04        21.07         7.99 
TCGA-D7-5577 TCGA-D7-5578 TCGA-D7-5579 TCGA-D7-6518 TCGA-D7-6519 TCGA-D7-6520 
        8.65         3.58         4.54         9.80        15.65         9.63 
TCGA-D7-6521 TCGA-D7-6522 TCGA-D7-6524 TCGA-D7-6525 TCGA-D7-6526 TCGA-D7-6527 
        8.19         6.90         0.69         5.95         6.61         4.14 
TCGA-D7-6528 TCGA-D7-6815 TCGA-D7-6817 TCGA-D7-6818 TCGA-D7-6822 TCGA-EQ-5647 
        1.68         3.65         4.70         4.04         4.27         0.62 
TCGA-EQ-8122 TCGA-F1-6177 TCGA-F1-6874 TCGA-F1-6875 TCGA-FP-7916 TCGA-FP-7998 
        7.79         6.54         2.01        72.23         3.02         3.58 
TCGA-FP-8099 TCGA-FP-8209 TCGA-FP-8210 TCGA-FP-8631 TCGA-HJ-7597 TCGA-IN-7806 
        1.02        59.05         5.03         0.56        26.43         6.87 

      12P GAIN CNV 12P GAIN WILD-TYPE 
              0.20               0.07 
      12P GAIN CNV 12P GAIN WILD-TYPE 
             31.04              72.23 
      12P GAIN CNV 12P GAIN WILD-TYPE 
             1.220              1.285 
[1] "0.2 - 31.0 (1.2)" "0.1 - 72.2 (1.3)"
        TCGA-B7-5816         TCGA-B7-5818         TCGA-BR-6452 
"12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" 
        TCGA-BR-6455         TCGA-BR-6457         TCGA-BR-6458 
"12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" 
        TCGA-BR-6563         TCGA-BR-6564         TCGA-BR-6565 
"12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" 
        TCGA-BR-6566         TCGA-BR-6705         TCGA-BR-6706 
"12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" 
        TCGA-BR-6707         TCGA-BR-6709         TCGA-BR-6710 
"12P GAIN WILD-TYPE"       "12P GAIN CNV" "12P GAIN WILD-TYPE" 
        TCGA-BR-6801         TCGA-BR-6802         TCGA-BR-6803 
      "12P GAIN CNV" "12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" 
        TCGA-BR-6852         TCGA-BR-7196         TCGA-BR-7197 
"12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" 
        TCGA-BR-7703         TCGA-BR-7704         TCGA-BR-7707 
"12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" 
        TCGA-BR-7715         TCGA-BR-7716         TCGA-BR-7717 
"12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" 
        TCGA-BR-7722         TCGA-BR-7723         TCGA-BR-7851 
"12P GAIN WILD-TYPE"       "12P GAIN CNV" "12P GAIN WILD-TYPE" 
        TCGA-BR-7901         TCGA-BR-7957         TCGA-BR-7958 
"12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" 
        TCGA-BR-7959         TCGA-BR-8059         TCGA-BR-8060 
      "12P GAIN CNV" "12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" 
        TCGA-BR-8077         TCGA-BR-8078         TCGA-BR-8080 
"12P GAIN WILD-TYPE"       "12P GAIN CNV" "12P GAIN WILD-TYPE" 
        TCGA-BR-8081         TCGA-BR-8284         TCGA-BR-8285 
"12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" 
        TCGA-BR-8286         TCGA-BR-8289         TCGA-BR-8291 
"12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" 
        TCGA-BR-8295         TCGA-BR-8296         TCGA-BR-8297 
      "12P GAIN CNV" "12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" 
        TCGA-BR-8592         TCGA-BR-A4IU         TCGA-BR-A4IV 
"12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" 
        TCGA-BR-A4IY         TCGA-BR-A4IZ         TCGA-BR-A4J1 
"12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE"       "12P GAIN CNV" 
        TCGA-BR-A4J2         TCGA-BR-A4J4         TCGA-BR-A4J5 
"12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" 
        TCGA-BR-A4J6         TCGA-BR-A4J8         TCGA-BR-A4J9 
"12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" 
        TCGA-BR-A4PF         TCGA-BR-A4QI         TCGA-BR-A4QL 
      "12P GAIN CNV" "12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" 
        TCGA-CD-5798         TCGA-CD-5799         TCGA-CD-5800 
"12P GAIN WILD-TYPE"       "12P GAIN CNV" "12P GAIN WILD-TYPE" 
        TCGA-CD-5801         TCGA-CD-5802         TCGA-CD-5803 
"12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" 
        TCGA-CG-4300         TCGA-CG-4301         TCGA-CG-4304 
"12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" 
        TCGA-CG-4305         TCGA-CG-4306         TCGA-CG-4436 
"12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" 
        TCGA-CG-4437         TCGA-CG-4438         TCGA-CG-4440 
"12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" 
        TCGA-CG-4441         TCGA-CG-4443         TCGA-CG-4444 
"12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" 
        TCGA-CG-4449         TCGA-CG-4455         TCGA-CG-4460 
"12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE"       "12P GAIN CNV" 
        TCGA-CG-4462         TCGA-CG-4465         TCGA-CG-4466 
"12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" 
        TCGA-CG-4469         TCGA-CG-4472         TCGA-CG-4474 
"12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" 
        TCGA-CG-4477         TCGA-CG-5716         TCGA-CG-5717 
"12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" 
        TCGA-CG-5718         TCGA-CG-5719         TCGA-CG-5720 
"12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" 
        TCGA-CG-5721         TCGA-CG-5722         TCGA-CG-5723 
"12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" 
        TCGA-CG-5724         TCGA-CG-5725         TCGA-CG-5726 
      "12P GAIN CNV" "12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" 
        TCGA-CG-5727         TCGA-CG-5728         TCGA-CG-5730 
      "12P GAIN CNV" "12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" 
        TCGA-CG-5732         TCGA-CG-5733         TCGA-CG-5734 
"12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" 
        TCGA-D7-5577         TCGA-D7-5578         TCGA-D7-5579 
"12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" 
        TCGA-D7-6518         TCGA-D7-6519         TCGA-D7-6520 
"12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" 
        TCGA-D7-6521         TCGA-D7-6522         TCGA-D7-6524 
"12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" 
        TCGA-D7-6525         TCGA-D7-6526         TCGA-D7-6527 
"12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" 
        TCGA-D7-6528         TCGA-D7-6815         TCGA-D7-6817 
"12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" 
        TCGA-D7-6818         TCGA-D7-6820         TCGA-D7-6822 
"12P GAIN WILD-TYPE"       "12P GAIN CNV" "12P GAIN WILD-TYPE" 
        TCGA-EQ-5647         TCGA-EQ-8122         TCGA-F1-6177 
"12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" 
        TCGA-F1-6874         TCGA-F1-6875         TCGA-FP-7735 
"12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE"       "12P GAIN CNV" 
        TCGA-FP-7829         TCGA-FP-7916         TCGA-FP-7998 
      "12P GAIN CNV" "12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" 
        TCGA-FP-8099         TCGA-FP-8209         TCGA-FP-8210 
"12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" 
        TCGA-FP-8631         TCGA-HJ-7597         TCGA-IN-7806 
"12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" 
        TCGA-IN-7808         TCGA-IP-7968 
      "12P GAIN CNV"       "12P GAIN CNV" 
        TCGA-B7-5816         TCGA-B7-5818         TCGA-BR-6452 
"12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" 
        TCGA-BR-6455         TCGA-BR-6457         TCGA-BR-6458 
"12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" 
        TCGA-BR-6563         TCGA-BR-6564         TCGA-BR-6565 
"12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" 
        TCGA-BR-6566         TCGA-BR-6705         TCGA-BR-6706 
"12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" 
        TCGA-BR-6707         TCGA-BR-6709         TCGA-BR-6710 
"12P GAIN WILD-TYPE"       "12P GAIN CNV" "12P GAIN WILD-TYPE" 
        TCGA-BR-6801         TCGA-BR-6802         TCGA-BR-6803 
      "12P GAIN CNV" "12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" 
        TCGA-BR-6852         TCGA-BR-7196         TCGA-BR-7197 
"12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" 
        TCGA-BR-7703         TCGA-BR-7704         TCGA-BR-7707 
"12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" 
        TCGA-BR-7715         TCGA-BR-7716         TCGA-BR-7717 
"12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" 
        TCGA-BR-7722         TCGA-BR-7723         TCGA-BR-7851 
"12P GAIN WILD-TYPE"       "12P GAIN CNV" "12P GAIN WILD-TYPE" 
        TCGA-BR-7901         TCGA-BR-7957         TCGA-BR-7958 
"12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" 
        TCGA-BR-7959         TCGA-BR-8059         TCGA-BR-8060 
      "12P GAIN CNV" "12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" 
        TCGA-BR-8077         TCGA-BR-8078         TCGA-BR-8080 
"12P GAIN WILD-TYPE"       "12P GAIN CNV" "12P GAIN WILD-TYPE" 
        TCGA-BR-8081         TCGA-BR-8284         TCGA-BR-8285 
"12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" 
        TCGA-BR-8286         TCGA-BR-8289         TCGA-BR-8291 
"12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" 
        TCGA-BR-8295         TCGA-BR-8296         TCGA-BR-8297 
      "12P GAIN CNV" "12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" 
        TCGA-BR-8592         TCGA-BR-A4IU         TCGA-BR-A4IV 
"12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" 
        TCGA-BR-A4IY         TCGA-BR-A4IZ         TCGA-BR-A4J1 
"12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE"       "12P GAIN CNV" 
        TCGA-BR-A4J2         TCGA-BR-A4J4         TCGA-BR-A4J5 
"12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" 
        TCGA-BR-A4J6         TCGA-BR-A4J8         TCGA-BR-A4J9 
"12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" 
        TCGA-BR-A4PF         TCGA-BR-A4QI         TCGA-BR-A4QL 
      "12P GAIN CNV" "12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" 
        TCGA-CD-5798         TCGA-CD-5799         TCGA-CD-5800 
"12P GAIN WILD-TYPE"       "12P GAIN CNV" "12P GAIN WILD-TYPE" 
        TCGA-CD-5801         TCGA-CD-5802         TCGA-CD-5803 
"12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" 
        TCGA-CG-4300         TCGA-CG-4301         TCGA-CG-4304 
"12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" 
        TCGA-CG-4305         TCGA-CG-4306         TCGA-CG-4436 
"12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" 
        TCGA-CG-4437         TCGA-CG-4438         TCGA-CG-4440 
"12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" 
        TCGA-CG-4441         TCGA-CG-4443         TCGA-CG-4444 
"12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" 
        TCGA-CG-4449         TCGA-CG-4455         TCGA-CG-4460 
"12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE"       "12P GAIN CNV" 
        TCGA-CG-4462         TCGA-CG-4465         TCGA-CG-4466 
"12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" 
        TCGA-CG-4469         TCGA-CG-4472         TCGA-CG-4474 
"12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" 
        TCGA-CG-4477         TCGA-CG-5716         TCGA-CG-5717 
"12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" 
        TCGA-CG-5718         TCGA-CG-5719         TCGA-CG-5720 
"12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" 
        TCGA-CG-5721         TCGA-CG-5722         TCGA-CG-5723 
"12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" 
        TCGA-CG-5724         TCGA-CG-5725         TCGA-CG-5726 
      "12P GAIN CNV" "12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" 
        TCGA-CG-5727         TCGA-CG-5728         TCGA-CG-5730 
      "12P GAIN CNV" "12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" 
        TCGA-CG-5732         TCGA-CG-5733         TCGA-CG-5734 
"12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" 
        TCGA-D7-5577         TCGA-D7-5578         TCGA-D7-5579 
"12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" 
        TCGA-D7-6518         TCGA-D7-6519         TCGA-D7-6520 
"12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" 
        TCGA-D7-6521         TCGA-D7-6522         TCGA-D7-6524 
"12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" 
        TCGA-D7-6525         TCGA-D7-6526         TCGA-D7-6527 
"12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" 
        TCGA-D7-6528         TCGA-D7-6815         TCGA-D7-6817 
"12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" 
        TCGA-D7-6818         TCGA-D7-6820         TCGA-D7-6822 
"12P GAIN WILD-TYPE"       "12P GAIN CNV" "12P GAIN WILD-TYPE" 
        TCGA-EQ-5647         TCGA-EQ-8122         TCGA-F1-6177 
"12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" 
        TCGA-F1-6874         TCGA-F1-6875         TCGA-FP-7735 
"12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE"       "12P GAIN CNV" 
        TCGA-FP-7829         TCGA-FP-7916         TCGA-FP-7998 
      "12P GAIN CNV" "12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" 
        TCGA-FP-8099         TCGA-FP-8209         TCGA-FP-8210 
"12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" 
        TCGA-FP-8631         TCGA-HJ-7597         TCGA-IN-7806 
"12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" 
        TCGA-IN-7808         TCGA-IP-7968 
      "12P GAIN CNV"       "12P GAIN CNV" 
        TCGA-B7-5816         TCGA-B7-5818         TCGA-BR-6452 
"12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" 
        TCGA-BR-6455         TCGA-BR-6457         TCGA-BR-6458 
"12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" 
        TCGA-BR-6563         TCGA-BR-6564         TCGA-BR-6565 
"12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" 
        TCGA-BR-6566         TCGA-BR-6705         TCGA-BR-6706 
"12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" 
        TCGA-BR-6707         TCGA-BR-6709         TCGA-BR-6710 
"12P GAIN WILD-TYPE"       "12P GAIN CNV" "12P GAIN WILD-TYPE" 
        TCGA-BR-6801         TCGA-BR-6802         TCGA-BR-6803 
      "12P GAIN CNV" "12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" 
        TCGA-BR-6852         TCGA-BR-7196         TCGA-BR-7197 
"12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" 
        TCGA-BR-7703         TCGA-BR-7704         TCGA-BR-7707 
"12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" 
        TCGA-BR-7715         TCGA-BR-7716         TCGA-BR-7717 
"12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" 
        TCGA-BR-7722         TCGA-BR-7723         TCGA-BR-7851 
"12P GAIN WILD-TYPE"       "12P GAIN CNV" "12P GAIN WILD-TYPE" 
        TCGA-BR-7901         TCGA-BR-7957         TCGA-BR-7958 
"12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" 
        TCGA-BR-7959         TCGA-BR-8059         TCGA-BR-8060 
      "12P GAIN CNV" "12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" 
        TCGA-BR-8077         TCGA-BR-8078         TCGA-BR-8080 
"12P GAIN WILD-TYPE"       "12P GAIN CNV" "12P GAIN WILD-TYPE" 
        TCGA-BR-8081         TCGA-BR-8284         TCGA-BR-8285 
"12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" 
        TCGA-BR-8286         TCGA-BR-8289         TCGA-BR-8291 
"12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" 
        TCGA-BR-8295         TCGA-BR-8296         TCGA-BR-8297 
      "12P GAIN CNV" "12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" 
        TCGA-BR-8592         TCGA-BR-A4IU         TCGA-BR-A4IV 
"12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" 
        TCGA-BR-A4IY         TCGA-BR-A4IZ         TCGA-BR-A4J1 
"12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE"       "12P GAIN CNV" 
        TCGA-BR-A4J2         TCGA-BR-A4J4         TCGA-BR-A4J5 
"12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" 
        TCGA-BR-A4J6         TCGA-BR-A4J8         TCGA-BR-A4J9 
"12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" 
        TCGA-BR-A4PF         TCGA-BR-A4QI         TCGA-BR-A4QL 
      "12P GAIN CNV" "12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" 
        TCGA-CD-5798         TCGA-CD-5799         TCGA-CD-5800 
"12P GAIN WILD-TYPE"       "12P GAIN CNV" "12P GAIN WILD-TYPE" 
        TCGA-CD-5801         TCGA-CD-5802         TCGA-CD-5803 
"12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" 
        TCGA-CG-4300         TCGA-CG-4301         TCGA-CG-4304 
"12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" 
        TCGA-CG-4305         TCGA-CG-4306         TCGA-CG-4436 
"12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" 
        TCGA-CG-4437         TCGA-CG-4438         TCGA-CG-4440 
"12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" 
        TCGA-CG-4441         TCGA-CG-4443         TCGA-CG-4444 
"12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" 
        TCGA-CG-4449         TCGA-CG-4455         TCGA-CG-4460 
"12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE"       "12P GAIN CNV" 
        TCGA-CG-4462         TCGA-CG-4465         TCGA-CG-4466 
"12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" 
        TCGA-CG-4469         TCGA-CG-4472         TCGA-CG-4474 
"12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" 
        TCGA-CG-4477         TCGA-CG-5716         TCGA-CG-5717 
"12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" 
        TCGA-CG-5718         TCGA-CG-5719         TCGA-CG-5720 
"12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" 
        TCGA-CG-5721         TCGA-CG-5722         TCGA-CG-5723 
"12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" 
        TCGA-CG-5724         TCGA-CG-5725         TCGA-CG-5726 
      "12P GAIN CNV" "12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" 
        TCGA-CG-5727         TCGA-CG-5728         TCGA-CG-5730 
      "12P GAIN CNV" "12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" 
        TCGA-CG-5732         TCGA-CG-5733         TCGA-CG-5734 
"12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" 
        TCGA-D7-5577         TCGA-D7-5578         TCGA-D7-5579 
"12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" 
        TCGA-D7-6518         TCGA-D7-6519         TCGA-D7-6520 
"12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" 
        TCGA-D7-6521         TCGA-D7-6522         TCGA-D7-6524 
"12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" 
        TCGA-D7-6525         TCGA-D7-6526         TCGA-D7-6527 
"12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" 
        TCGA-D7-6528         TCGA-D7-6815         TCGA-D7-6817 
"12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" 
        TCGA-D7-6818         TCGA-D7-6820         TCGA-D7-6822 
"12P GAIN WILD-TYPE"       "12P GAIN CNV" "12P GAIN WILD-TYPE" 
        TCGA-EQ-5647         TCGA-EQ-8122         TCGA-F1-6177 
"12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" 
        TCGA-F1-6874         TCGA-F1-6875         TCGA-FP-7735 
"12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE"       "12P GAIN CNV" 
        TCGA-FP-7829         TCGA-FP-7916         TCGA-FP-7998 
      "12P GAIN CNV" "12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" 
        TCGA-FP-8099         TCGA-FP-8209         TCGA-FP-8210 
"12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" 
        TCGA-FP-8631         TCGA-HJ-7597         TCGA-IN-7806 
"12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" 
        TCGA-IN-7808         TCGA-IP-7968 
      "12P GAIN CNV"       "12P GAIN CNV" 
[1] "hr=" "1.8"
D22V2, continuous
D22V3, binary
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  12P GAIN CNV          5   15
  12P GAIN WILD-TYPE   67   93
        clus
vv       12P GAIN CNV 12P GAIN WILD-TYPE
  FEMALE            5                 67
  MALE             15                 93
                    vv
clus                 STOMACH  ADENOCARCINOMA  DIFFUSE TYPE
  12P GAIN CNV                                           0
  12P GAIN WILD-TYPE                                    10
                    vv
clus                 STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  12P GAIN CNV                                                            4
  12P GAIN WILD-TYPE                                                     12
                    vv
clus                 STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  12P GAIN CNV                                                                       0
  12P GAIN WILD-TYPE                                                                 8
                    vv
clus                 STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE
  12P GAIN CNV                                                              1
  12P GAIN WILD-TYPE                                                        2
                    vv
clus                 STOMACH ADENOCARCINOMA  SIGNET RING TYPE
  12P GAIN CNV                                              0
  12P GAIN WILD-TYPE                                        1
                    vv
clus                 STOMACH ADENOCARCINOMA - DIFFUSE TYPE
  12P GAIN CNV                                           2
  12P GAIN WILD-TYPE                                    14
                    vv
clus                 STOMACH ADENOCARCINOMA - NOT OTHERWISE SPECIFIED (NOS)
  12P GAIN CNV                                                            7
  12P GAIN WILD-TYPE                                                     66
                    vv
clus                 STOMACH INTESTINAL ADENOCARCINOMA - MUCINOUS TYPE
  12P GAIN CNV                                                       1
  12P GAIN WILD-TYPE                                                 6
                    vv
clus                 STOMACH INTESTINAL ADENOCARCINOMA - PAPILLARY TYPE
  12P GAIN CNV                                                        0
  12P GAIN WILD-TYPE                                                  3
                    vv
clus                 STOMACH INTESTINAL ADENOCARCINOMA - TUBULAR TYPE
  12P GAIN CNV                                                      1
  12P GAIN WILD-TYPE                                                9
                    vv
clus                 STOMACH INTESTINAL ADENOCARCINOMA - TYPE NOT OTHERWISE SPECIFIED (NOS)
  12P GAIN CNV                                                                            3
  12P GAIN WILD-TYPE                                                                     25
D22V4, multiclass
                    vv
clus                 T1 T2 T3 T4
  12P GAIN CNV        0  3  9  3
  12P GAIN WILD-TYPE  6 49 47 15
D22V5, multiclass
    clus
vv   12P GAIN CNV 12P GAIN WILD-TYPE
  T1            0                  6
  T2            3                 49
  T3            9                 47
  T4            3                 15
                    vv
clus                 N0 N1 N2 N3
  12P GAIN CNV        4  5  4  2
  12P GAIN WILD-TYPE 40 44 19 13
D22V6, multiclass
    clus
vv   12P GAIN CNV 12P GAIN WILD-TYPE
  N0            4                 40
  N1            5                 44
  N2            4                 19
  N3            2                 13
                    vv
clus                  M0  M1  MX
  12P GAIN CNV        10   3   2
  12P GAIN WILD-TYPE 108  13   6
D22V7, multiclass
    clus
vv   12P GAIN CNV 12P GAIN WILD-TYPE
  M0           10                108
  M1            3                 13
  MX            2                  6
                    vv
clus                  I II III IV
  12P GAIN CNV        1  6   5  3
  12P GAIN WILD-TYPE 23 31  34 23
D22V8, multiclass
     clus
vv    12P GAIN CNV 12P GAIN WILD-TYPE
  I              1                 23
  II             6                 31
  III            5                 34
  IV             3                 23
D22V9, binary
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  12P GAIN CNV          0   20
  12P GAIN WILD-TYPE    5  155
     clus
vv    12P GAIN CNV 12P GAIN WILD-TYPE
  NO             0                  5
  YES           20                155
                    vv
clus                  R0  R1  R2  RX
  12P GAIN CNV        13   1   2   1
  12P GAIN WILD-TYPE 112   6  10  24
D22V10, multiclass
    clus
vv   12P GAIN CNV 12P GAIN WILD-TYPE
  R0           13                112
  R1            1                  6
  R2            2                 10
  RX            1                 24
D22V11, continuous

Clustering(23) Variable = 12q gain
D23V1, survival
                    sevent
clus2                  0   1
  12Q GAIN CNV        11   2
  12Q GAIN WILD-TYPE 113  17
      12Q GAIN CNV 12Q GAIN WILD-TYPE 
                13                130 
      12Q GAIN CNV 12Q GAIN WILD-TYPE 
                 2                 17 
$`12Q GAIN CNV`
TCGA-BR-6709 TCGA-BR-7723 TCGA-BR-7959 TCGA-BR-8078 TCGA-BR-8295 TCGA-BR-A4J1 
        1.22         4.54         1.08         0.95         1.55         0.72 
TCGA-BR-A4J4 TCGA-CD-5799 TCGA-CG-4460 TCGA-CG-4472 TCGA-CG-5727 TCGA-D7-6527 
        0.53         0.69        21.99        12.00        31.04         4.14 
TCGA-IP-7968 
        2.53 

$`12Q GAIN WILD-TYPE`
TCGA-B7-5816 TCGA-B7-5818 TCGA-BR-6452 TCGA-BR-6455 TCGA-BR-6457 TCGA-BR-6458 
        5.62         0.10         0.95         1.41         1.35         1.35 
TCGA-BR-6563 TCGA-BR-6564 TCGA-BR-6565 TCGA-BR-6566 TCGA-BR-6705 TCGA-BR-6706 
        0.85         0.82         0.62         0.62         1.71         2.17 
TCGA-BR-6707 TCGA-BR-6710 TCGA-BR-6801 TCGA-BR-6802 TCGA-BR-6803 TCGA-BR-6852 
        0.99         0.66         1.12         0.76         0.66         0.26 
TCGA-BR-7196 TCGA-BR-7197 TCGA-BR-7703 TCGA-BR-7704 TCGA-BR-7707 TCGA-BR-7715 
        1.22         1.48         0.46         1.25         0.13         1.05 
TCGA-BR-7716 TCGA-BR-7717 TCGA-BR-7722 TCGA-BR-7851 TCGA-BR-7901 TCGA-BR-7957 
        0.82         0.69         0.16         0.99         0.95         0.69 
TCGA-BR-7958 TCGA-BR-8059 TCGA-BR-8060 TCGA-BR-8077 TCGA-BR-8080 TCGA-BR-8081 
        0.16         0.82         1.32         0.69         0.49         0.46 
TCGA-BR-8284 TCGA-BR-8285 TCGA-BR-8286 TCGA-BR-8289 TCGA-BR-8291 TCGA-BR-8296 
        0.72         0.26         0.43         0.26         1.18         1.48 
TCGA-BR-8297 TCGA-BR-8592 TCGA-BR-A4IU TCGA-BR-A4IV TCGA-BR-A4IY TCGA-BR-A4IZ 
        0.76         0.20         0.59         0.92         0.39         0.79 
TCGA-BR-A4J2 TCGA-BR-A4J5 TCGA-BR-A4J6 TCGA-BR-A4J8 TCGA-BR-A4J9 TCGA-BR-A4PF 
        0.79         0.43         0.13         0.23         0.10         0.72 
TCGA-BR-A4QI TCGA-BR-A4QL TCGA-CD-5798 TCGA-CD-5800 TCGA-CD-5801 TCGA-CD-5802 
        0.49         2.24         0.82         0.36         0.49         0.30 
TCGA-CD-5803 TCGA-CG-4300 TCGA-CG-4301 TCGA-CG-4304 TCGA-CG-4305 TCGA-CG-4306 
        0.07        20.02         3.02        27.02        15.95         1.02 
TCGA-CG-4436 TCGA-CG-4437 TCGA-CG-4438 TCGA-CG-4440 TCGA-CG-4441 TCGA-CG-4443 
       52.96         8.05        54.05         4.01        14.01        29.98 
TCGA-CG-4444 TCGA-CG-4449 TCGA-CG-4455 TCGA-CG-4462 TCGA-CG-4465 TCGA-CG-4466 
       47.05        19.07        12.03         1.02         8.98        18.94 
TCGA-CG-4469 TCGA-CG-4474 TCGA-CG-4477 TCGA-CG-5716 TCGA-CG-5717 TCGA-CG-5718 
        7.07         1.02         1.02         1.02         6.94         1.02 
TCGA-CG-5719 TCGA-CG-5720 TCGA-CG-5721 TCGA-CG-5722 TCGA-CG-5723 TCGA-CG-5724 
        1.02         0.99         5.98         0.95        70.06        12.03 
TCGA-CG-5725 TCGA-CG-5726 TCGA-CG-5728 TCGA-CG-5730 TCGA-CG-5732 TCGA-CG-5733 
       15.02        28.96        65.10         4.01        55.04        21.07 
TCGA-CG-5734 TCGA-D7-5577 TCGA-D7-5578 TCGA-D7-5579 TCGA-D7-6518 TCGA-D7-6519 
        7.99         8.65         3.58         4.54         9.80        15.65 
TCGA-D7-6520 TCGA-D7-6521 TCGA-D7-6522 TCGA-D7-6524 TCGA-D7-6525 TCGA-D7-6526 
        9.63         8.19         6.90         0.69         5.95         6.61 
TCGA-D7-6528 TCGA-D7-6815 TCGA-D7-6817 TCGA-D7-6818 TCGA-D7-6820 TCGA-D7-6822 
        1.68         3.65         4.70         4.04         2.93         4.27 
TCGA-EQ-5647 TCGA-EQ-8122 TCGA-F1-6177 TCGA-F1-6874 TCGA-F1-6875 TCGA-FP-7735 
        0.62         7.79         6.54         2.01        72.23         0.39 
TCGA-FP-7829 TCGA-FP-7916 TCGA-FP-7998 TCGA-FP-8099 TCGA-FP-8209 TCGA-FP-8210 
        0.20         3.02         3.58         1.02        59.05         5.03 
TCGA-FP-8631 TCGA-HJ-7597 TCGA-IN-7806 TCGA-IN-7808 
        0.56        26.43         6.87         3.55 

      12Q GAIN CNV 12Q GAIN WILD-TYPE 
              0.53               0.07 
      12Q GAIN CNV 12Q GAIN WILD-TYPE 
             31.04              72.23 
      12Q GAIN CNV 12Q GAIN WILD-TYPE 
             1.550              1.235 
[1] "0.5 - 31.0 (1.6)" "0.1 - 72.2 (1.2)"
        TCGA-B7-5816         TCGA-B7-5818         TCGA-BR-6452 
"12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" 
        TCGA-BR-6455         TCGA-BR-6457         TCGA-BR-6458 
"12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" 
        TCGA-BR-6563         TCGA-BR-6564         TCGA-BR-6565 
"12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" 
        TCGA-BR-6566         TCGA-BR-6705         TCGA-BR-6706 
"12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" 
        TCGA-BR-6707         TCGA-BR-6709         TCGA-BR-6710 
"12Q GAIN WILD-TYPE"       "12Q GAIN CNV" "12Q GAIN WILD-TYPE" 
        TCGA-BR-6801         TCGA-BR-6802         TCGA-BR-6803 
"12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" 
        TCGA-BR-6852         TCGA-BR-7196         TCGA-BR-7197 
"12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" 
        TCGA-BR-7703         TCGA-BR-7704         TCGA-BR-7707 
"12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" 
        TCGA-BR-7715         TCGA-BR-7716         TCGA-BR-7717 
"12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" 
        TCGA-BR-7722         TCGA-BR-7723         TCGA-BR-7851 
"12Q GAIN WILD-TYPE"       "12Q GAIN CNV" "12Q GAIN WILD-TYPE" 
        TCGA-BR-7901         TCGA-BR-7957         TCGA-BR-7958 
"12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" 
        TCGA-BR-7959         TCGA-BR-8059         TCGA-BR-8060 
      "12Q GAIN CNV" "12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" 
        TCGA-BR-8077         TCGA-BR-8078         TCGA-BR-8080 
"12Q GAIN WILD-TYPE"       "12Q GAIN CNV" "12Q GAIN WILD-TYPE" 
        TCGA-BR-8081         TCGA-BR-8284         TCGA-BR-8285 
"12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" 
        TCGA-BR-8286         TCGA-BR-8289         TCGA-BR-8291 
"12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" 
        TCGA-BR-8295         TCGA-BR-8296         TCGA-BR-8297 
      "12Q GAIN CNV" "12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" 
        TCGA-BR-8592         TCGA-BR-A4IU         TCGA-BR-A4IV 
"12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" 
        TCGA-BR-A4IY         TCGA-BR-A4IZ         TCGA-BR-A4J1 
"12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE"       "12Q GAIN CNV" 
        TCGA-BR-A4J2         TCGA-BR-A4J4         TCGA-BR-A4J5 
"12Q GAIN WILD-TYPE"       "12Q GAIN CNV" "12Q GAIN WILD-TYPE" 
        TCGA-BR-A4J6         TCGA-BR-A4J8         TCGA-BR-A4J9 
"12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" 
        TCGA-BR-A4PF         TCGA-BR-A4QI         TCGA-BR-A4QL 
"12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" 
        TCGA-CD-5798         TCGA-CD-5799         TCGA-CD-5800 
"12Q GAIN WILD-TYPE"       "12Q GAIN CNV" "12Q GAIN WILD-TYPE" 
        TCGA-CD-5801         TCGA-CD-5802         TCGA-CD-5803 
"12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" 
        TCGA-CG-4300         TCGA-CG-4301         TCGA-CG-4304 
"12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" 
        TCGA-CG-4305         TCGA-CG-4306         TCGA-CG-4436 
"12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" 
        TCGA-CG-4437         TCGA-CG-4438         TCGA-CG-4440 
"12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" 
        TCGA-CG-4441         TCGA-CG-4443         TCGA-CG-4444 
"12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" 
        TCGA-CG-4449         TCGA-CG-4455         TCGA-CG-4460 
"12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE"       "12Q GAIN CNV" 
        TCGA-CG-4462         TCGA-CG-4465         TCGA-CG-4466 
"12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" 
        TCGA-CG-4469         TCGA-CG-4472         TCGA-CG-4474 
"12Q GAIN WILD-TYPE"       "12Q GAIN CNV" "12Q GAIN WILD-TYPE" 
        TCGA-CG-4477         TCGA-CG-5716         TCGA-CG-5717 
"12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" 
        TCGA-CG-5718         TCGA-CG-5719         TCGA-CG-5720 
"12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" 
        TCGA-CG-5721         TCGA-CG-5722         TCGA-CG-5723 
"12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" 
        TCGA-CG-5724         TCGA-CG-5725         TCGA-CG-5726 
"12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" 
        TCGA-CG-5727         TCGA-CG-5728         TCGA-CG-5730 
      "12Q GAIN CNV" "12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" 
        TCGA-CG-5732         TCGA-CG-5733         TCGA-CG-5734 
"12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" 
        TCGA-D7-5577         TCGA-D7-5578         TCGA-D7-5579 
"12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" 
        TCGA-D7-6518         TCGA-D7-6519         TCGA-D7-6520 
"12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" 
        TCGA-D7-6521         TCGA-D7-6522         TCGA-D7-6524 
"12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" 
        TCGA-D7-6525         TCGA-D7-6526         TCGA-D7-6527 
"12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE"       "12Q GAIN CNV" 
        TCGA-D7-6528         TCGA-D7-6815         TCGA-D7-6817 
"12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" 
        TCGA-D7-6818         TCGA-D7-6820         TCGA-D7-6822 
"12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" 
        TCGA-EQ-5647         TCGA-EQ-8122         TCGA-F1-6177 
"12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" 
        TCGA-F1-6874         TCGA-F1-6875         TCGA-FP-7735 
"12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" 
        TCGA-FP-7829         TCGA-FP-7916         TCGA-FP-7998 
"12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" 
        TCGA-FP-8099         TCGA-FP-8209         TCGA-FP-8210 
"12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" 
        TCGA-FP-8631         TCGA-HJ-7597         TCGA-IN-7806 
"12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" 
        TCGA-IN-7808         TCGA-IP-7968 
"12Q GAIN WILD-TYPE"       "12Q GAIN CNV" 
        TCGA-B7-5816         TCGA-B7-5818         TCGA-BR-6452 
"12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" 
        TCGA-BR-6455         TCGA-BR-6457         TCGA-BR-6458 
"12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" 
        TCGA-BR-6563         TCGA-BR-6564         TCGA-BR-6565 
"12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" 
        TCGA-BR-6566         TCGA-BR-6705         TCGA-BR-6706 
"12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" 
        TCGA-BR-6707         TCGA-BR-6709         TCGA-BR-6710 
"12Q GAIN WILD-TYPE"       "12Q GAIN CNV" "12Q GAIN WILD-TYPE" 
        TCGA-BR-6801         TCGA-BR-6802         TCGA-BR-6803 
"12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" 
        TCGA-BR-6852         TCGA-BR-7196         TCGA-BR-7197 
"12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" 
        TCGA-BR-7703         TCGA-BR-7704         TCGA-BR-7707 
"12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" 
        TCGA-BR-7715         TCGA-BR-7716         TCGA-BR-7717 
"12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" 
        TCGA-BR-7722         TCGA-BR-7723         TCGA-BR-7851 
"12Q GAIN WILD-TYPE"       "12Q GAIN CNV" "12Q GAIN WILD-TYPE" 
        TCGA-BR-7901         TCGA-BR-7957         TCGA-BR-7958 
"12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" 
        TCGA-BR-7959         TCGA-BR-8059         TCGA-BR-8060 
      "12Q GAIN CNV" "12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" 
        TCGA-BR-8077         TCGA-BR-8078         TCGA-BR-8080 
"12Q GAIN WILD-TYPE"       "12Q GAIN CNV" "12Q GAIN WILD-TYPE" 
        TCGA-BR-8081         TCGA-BR-8284         TCGA-BR-8285 
"12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" 
        TCGA-BR-8286         TCGA-BR-8289         TCGA-BR-8291 
"12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" 
        TCGA-BR-8295         TCGA-BR-8296         TCGA-BR-8297 
      "12Q GAIN CNV" "12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" 
        TCGA-BR-8592         TCGA-BR-A4IU         TCGA-BR-A4IV 
"12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" 
        TCGA-BR-A4IY         TCGA-BR-A4IZ         TCGA-BR-A4J1 
"12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE"       "12Q GAIN CNV" 
        TCGA-BR-A4J2         TCGA-BR-A4J4         TCGA-BR-A4J5 
"12Q GAIN WILD-TYPE"       "12Q GAIN CNV" "12Q GAIN WILD-TYPE" 
        TCGA-BR-A4J6         TCGA-BR-A4J8         TCGA-BR-A4J9 
"12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" 
        TCGA-BR-A4PF         TCGA-BR-A4QI         TCGA-BR-A4QL 
"12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" 
        TCGA-CD-5798         TCGA-CD-5799         TCGA-CD-5800 
"12Q GAIN WILD-TYPE"       "12Q GAIN CNV" "12Q GAIN WILD-TYPE" 
        TCGA-CD-5801         TCGA-CD-5802         TCGA-CD-5803 
"12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" 
        TCGA-CG-4300         TCGA-CG-4301         TCGA-CG-4304 
"12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" 
        TCGA-CG-4305         TCGA-CG-4306         TCGA-CG-4436 
"12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" 
        TCGA-CG-4437         TCGA-CG-4438         TCGA-CG-4440 
"12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" 
        TCGA-CG-4441         TCGA-CG-4443         TCGA-CG-4444 
"12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" 
        TCGA-CG-4449         TCGA-CG-4455         TCGA-CG-4460 
"12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE"       "12Q GAIN CNV" 
        TCGA-CG-4462         TCGA-CG-4465         TCGA-CG-4466 
"12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" 
        TCGA-CG-4469         TCGA-CG-4472         TCGA-CG-4474 
"12Q GAIN WILD-TYPE"       "12Q GAIN CNV" "12Q GAIN WILD-TYPE" 
        TCGA-CG-4477         TCGA-CG-5716         TCGA-CG-5717 
"12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" 
        TCGA-CG-5718         TCGA-CG-5719         TCGA-CG-5720 
"12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" 
        TCGA-CG-5721         TCGA-CG-5722         TCGA-CG-5723 
"12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" 
        TCGA-CG-5724         TCGA-CG-5725         TCGA-CG-5726 
"12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" 
        TCGA-CG-5727         TCGA-CG-5728         TCGA-CG-5730 
      "12Q GAIN CNV" "12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" 
        TCGA-CG-5732         TCGA-CG-5733         TCGA-CG-5734 
"12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" 
        TCGA-D7-5577         TCGA-D7-5578         TCGA-D7-5579 
"12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" 
        TCGA-D7-6518         TCGA-D7-6519         TCGA-D7-6520 
"12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" 
        TCGA-D7-6521         TCGA-D7-6522         TCGA-D7-6524 
"12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" 
        TCGA-D7-6525         TCGA-D7-6526         TCGA-D7-6527 
"12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE"       "12Q GAIN CNV" 
        TCGA-D7-6528         TCGA-D7-6815         TCGA-D7-6817 
"12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" 
        TCGA-D7-6818         TCGA-D7-6820         TCGA-D7-6822 
"12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" 
        TCGA-EQ-5647         TCGA-EQ-8122         TCGA-F1-6177 
"12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" 
        TCGA-F1-6874         TCGA-F1-6875         TCGA-FP-7735 
"12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" 
        TCGA-FP-7829         TCGA-FP-7916         TCGA-FP-7998 
"12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" 
        TCGA-FP-8099         TCGA-FP-8209         TCGA-FP-8210 
"12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" 
        TCGA-FP-8631         TCGA-HJ-7597         TCGA-IN-7806 
"12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" 
        TCGA-IN-7808         TCGA-IP-7968 
"12Q GAIN WILD-TYPE"       "12Q GAIN CNV" 
        TCGA-B7-5816         TCGA-B7-5818         TCGA-BR-6452 
"12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" 
        TCGA-BR-6455         TCGA-BR-6457         TCGA-BR-6458 
"12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" 
        TCGA-BR-6563         TCGA-BR-6564         TCGA-BR-6565 
"12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" 
        TCGA-BR-6566         TCGA-BR-6705         TCGA-BR-6706 
"12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" 
        TCGA-BR-6707         TCGA-BR-6709         TCGA-BR-6710 
"12Q GAIN WILD-TYPE"       "12Q GAIN CNV" "12Q GAIN WILD-TYPE" 
        TCGA-BR-6801         TCGA-BR-6802         TCGA-BR-6803 
"12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" 
        TCGA-BR-6852         TCGA-BR-7196         TCGA-BR-7197 
"12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" 
        TCGA-BR-7703         TCGA-BR-7704         TCGA-BR-7707 
"12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" 
        TCGA-BR-7715         TCGA-BR-7716         TCGA-BR-7717 
"12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" 
        TCGA-BR-7722         TCGA-BR-7723         TCGA-BR-7851 
"12Q GAIN WILD-TYPE"       "12Q GAIN CNV" "12Q GAIN WILD-TYPE" 
        TCGA-BR-7901         TCGA-BR-7957         TCGA-BR-7958 
"12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" 
        TCGA-BR-7959         TCGA-BR-8059         TCGA-BR-8060 
      "12Q GAIN CNV" "12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" 
        TCGA-BR-8077         TCGA-BR-8078         TCGA-BR-8080 
"12Q GAIN WILD-TYPE"       "12Q GAIN CNV" "12Q GAIN WILD-TYPE" 
        TCGA-BR-8081         TCGA-BR-8284         TCGA-BR-8285 
"12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" 
        TCGA-BR-8286         TCGA-BR-8289         TCGA-BR-8291 
"12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" 
        TCGA-BR-8295         TCGA-BR-8296         TCGA-BR-8297 
      "12Q GAIN CNV" "12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" 
        TCGA-BR-8592         TCGA-BR-A4IU         TCGA-BR-A4IV 
"12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" 
        TCGA-BR-A4IY         TCGA-BR-A4IZ         TCGA-BR-A4J1 
"12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE"       "12Q GAIN CNV" 
        TCGA-BR-A4J2         TCGA-BR-A4J4         TCGA-BR-A4J5 
"12Q GAIN WILD-TYPE"       "12Q GAIN CNV" "12Q GAIN WILD-TYPE" 
        TCGA-BR-A4J6         TCGA-BR-A4J8         TCGA-BR-A4J9 
"12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" 
        TCGA-BR-A4PF         TCGA-BR-A4QI         TCGA-BR-A4QL 
"12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" 
        TCGA-CD-5798         TCGA-CD-5799         TCGA-CD-5800 
"12Q GAIN WILD-TYPE"       "12Q GAIN CNV" "12Q GAIN WILD-TYPE" 
        TCGA-CD-5801         TCGA-CD-5802         TCGA-CD-5803 
"12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" 
        TCGA-CG-4300         TCGA-CG-4301         TCGA-CG-4304 
"12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" 
        TCGA-CG-4305         TCGA-CG-4306         TCGA-CG-4436 
"12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" 
        TCGA-CG-4437         TCGA-CG-4438         TCGA-CG-4440 
"12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" 
        TCGA-CG-4441         TCGA-CG-4443         TCGA-CG-4444 
"12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" 
        TCGA-CG-4449         TCGA-CG-4455         TCGA-CG-4460 
"12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE"       "12Q GAIN CNV" 
        TCGA-CG-4462         TCGA-CG-4465         TCGA-CG-4466 
"12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" 
        TCGA-CG-4469         TCGA-CG-4472         TCGA-CG-4474 
"12Q GAIN WILD-TYPE"       "12Q GAIN CNV" "12Q GAIN WILD-TYPE" 
        TCGA-CG-4477         TCGA-CG-5716         TCGA-CG-5717 
"12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" 
        TCGA-CG-5718         TCGA-CG-5719         TCGA-CG-5720 
"12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" 
        TCGA-CG-5721         TCGA-CG-5722         TCGA-CG-5723 
"12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" 
        TCGA-CG-5724         TCGA-CG-5725         TCGA-CG-5726 
"12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" 
        TCGA-CG-5727         TCGA-CG-5728         TCGA-CG-5730 
      "12Q GAIN CNV" "12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" 
        TCGA-CG-5732         TCGA-CG-5733         TCGA-CG-5734 
"12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" 
        TCGA-D7-5577         TCGA-D7-5578         TCGA-D7-5579 
"12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" 
        TCGA-D7-6518         TCGA-D7-6519         TCGA-D7-6520 
"12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" 
        TCGA-D7-6521         TCGA-D7-6522         TCGA-D7-6524 
"12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" 
        TCGA-D7-6525         TCGA-D7-6526         TCGA-D7-6527 
"12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE"       "12Q GAIN CNV" 
        TCGA-D7-6528         TCGA-D7-6815         TCGA-D7-6817 
"12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" 
        TCGA-D7-6818         TCGA-D7-6820         TCGA-D7-6822 
"12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" 
        TCGA-EQ-5647         TCGA-EQ-8122         TCGA-F1-6177 
"12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" 
        TCGA-F1-6874         TCGA-F1-6875         TCGA-FP-7735 
"12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" 
        TCGA-FP-7829         TCGA-FP-7916         TCGA-FP-7998 
"12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" 
        TCGA-FP-8099         TCGA-FP-8209         TCGA-FP-8210 
"12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" 
        TCGA-FP-8631         TCGA-HJ-7597         TCGA-IN-7806 
"12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" 
        TCGA-IN-7808         TCGA-IP-7968 
"12Q GAIN WILD-TYPE"       "12Q GAIN CNV" 
[1] "hr=" "1.2"
D23V2, continuous
D23V3, binary
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  12Q GAIN CNV          5   10
  12Q GAIN WILD-TYPE   67   98
        clus
vv       12Q GAIN CNV 12Q GAIN WILD-TYPE
  FEMALE            5                 67
  MALE             10                 98
                    vv
clus                 STOMACH  ADENOCARCINOMA  DIFFUSE TYPE
  12Q GAIN CNV                                           0
  12Q GAIN WILD-TYPE                                    10
                    vv
clus                 STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  12Q GAIN CNV                                                            4
  12Q GAIN WILD-TYPE                                                     12
                    vv
clus                 STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  12Q GAIN CNV                                                                       0
  12Q GAIN WILD-TYPE                                                                 8
                    vv
clus                 STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE
  12Q GAIN CNV                                                              1
  12Q GAIN WILD-TYPE                                                        2
                    vv
clus                 STOMACH ADENOCARCINOMA  SIGNET RING TYPE
  12Q GAIN CNV                                              0
  12Q GAIN WILD-TYPE                                        1
                    vv
clus                 STOMACH ADENOCARCINOMA - DIFFUSE TYPE
  12Q GAIN CNV                                           0
  12Q GAIN WILD-TYPE                                    16
                    vv
clus                 STOMACH ADENOCARCINOMA - NOT OTHERWISE SPECIFIED (NOS)
  12Q GAIN CNV                                                            5
  12Q GAIN WILD-TYPE                                                     68
                    vv
clus                 STOMACH INTESTINAL ADENOCARCINOMA - MUCINOUS TYPE
  12Q GAIN CNV                                                       0
  12Q GAIN WILD-TYPE                                                 7
                    vv
clus                 STOMACH INTESTINAL ADENOCARCINOMA - PAPILLARY TYPE
  12Q GAIN CNV                                                        1
  12Q GAIN WILD-TYPE                                                  2
                    vv
clus                 STOMACH INTESTINAL ADENOCARCINOMA - TUBULAR TYPE
  12Q GAIN CNV                                                      0
  12Q GAIN WILD-TYPE                                               10
                    vv
clus                 STOMACH INTESTINAL ADENOCARCINOMA - TYPE NOT OTHERWISE SPECIFIED (NOS)
  12Q GAIN CNV                                                                            3
  12Q GAIN WILD-TYPE                                                                     25
D23V4, multiclass
                    vv
clus                 T1 T2 T3 T4
  12Q GAIN CNV        0  3  4  3
  12Q GAIN WILD-TYPE  6 49 52 15
D23V5, multiclass
    clus
vv   12Q GAIN CNV 12Q GAIN WILD-TYPE
  T1            0                  6
  T2            3                 49
  T3            4                 52
  T4            3                 15
                    vv
clus                 N0 N1 N2 N3
  12Q GAIN CNV        2  4  4  0
  12Q GAIN WILD-TYPE 42 45 19 15
D23V6, multiclass
    clus
vv   12Q GAIN CNV 12Q GAIN WILD-TYPE
  N0            2                 42
  N1            4                 45
  N2            4                 19
  N3            0                 15
                    vv
clus                  M0  M1  MX
  12Q GAIN CNV         8   1   1
  12Q GAIN WILD-TYPE 110  15   7
D23V7, multiclass
    clus
vv   12Q GAIN CNV 12Q GAIN WILD-TYPE
  M0            8                110
  M1            1                 15
  MX            1                  7
                    vv
clus                  I II III IV
  12Q GAIN CNV        1  4   2  3
  12Q GAIN WILD-TYPE 23 33  37 23
D23V8, multiclass
     clus
vv    12Q GAIN CNV 12Q GAIN WILD-TYPE
  I              1                 23
  II             4                 33
  III            2                 37
  IV             3                 23
D23V9, binary
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  12Q GAIN CNV          1   14
  12Q GAIN WILD-TYPE    4  161
     clus
vv    12Q GAIN CNV 12Q GAIN WILD-TYPE
  NO             1                  4
  YES           14                161
                    vv
clus                  R0  R1  R2  RX
  12Q GAIN CNV         9   1   1   2
  12Q GAIN WILD-TYPE 116   6  11  23
D23V10, multiclass
    clus
vv   12Q GAIN CNV 12Q GAIN WILD-TYPE
  R0            9                116
  R1            1                  6
  R2            1                 11
  RX            2                 23
D23V11, continuous

Clustering(24) Variable = 13q gain
D24V1, survival
                    sevent
clus2                 0  1
  13Q GAIN CNV       26  4
  13Q GAIN WILD-TYPE 98 15
      13Q GAIN CNV 13Q GAIN WILD-TYPE 
                30                113 
      13Q GAIN CNV 13Q GAIN WILD-TYPE 
                 4                 15 
$`13Q GAIN CNV`
TCGA-B7-5818 TCGA-BR-6565 TCGA-BR-6705 TCGA-BR-6801 TCGA-BR-7197 TCGA-BR-7704 
        0.10         0.62         1.71         1.12         1.48         1.25 
TCGA-BR-7717 TCGA-BR-7723 TCGA-BR-8077 TCGA-BR-8078 TCGA-BR-A4J1 TCGA-BR-A4J8 
        0.69         4.54         0.69         0.95         0.72         0.23 
TCGA-BR-A4PF TCGA-CD-5799 TCGA-CD-5800 TCGA-CG-4300 TCGA-CG-4305 TCGA-CG-4436 
        0.72         0.69         0.36        20.02        15.95        52.96 
TCGA-CG-4469 TCGA-CG-4472 TCGA-CG-5730 TCGA-CG-5732 TCGA-D7-5577 TCGA-D7-6518 
        7.07        12.00         4.01        55.04         8.65         9.80 
TCGA-D7-6526 TCGA-D7-6527 TCGA-D7-6820 TCGA-EQ-5647 TCGA-F1-6875 TCGA-FP-7829 
        6.61         4.14         2.93         0.62        72.23         0.20 

$`13Q GAIN WILD-TYPE`
TCGA-B7-5816 TCGA-BR-6452 TCGA-BR-6455 TCGA-BR-6457 TCGA-BR-6458 TCGA-BR-6563 
        5.62         0.95         1.41         1.35         1.35         0.85 
TCGA-BR-6564 TCGA-BR-6566 TCGA-BR-6706 TCGA-BR-6707 TCGA-BR-6709 TCGA-BR-6710 
        0.82         0.62         2.17         0.99         1.22         0.66 
TCGA-BR-6802 TCGA-BR-6803 TCGA-BR-6852 TCGA-BR-7196 TCGA-BR-7703 TCGA-BR-7707 
        0.76         0.66         0.26         1.22         0.46         0.13 
TCGA-BR-7715 TCGA-BR-7716 TCGA-BR-7722 TCGA-BR-7851 TCGA-BR-7901 TCGA-BR-7957 
        1.05         0.82         0.16         0.99         0.95         0.69 
TCGA-BR-7958 TCGA-BR-7959 TCGA-BR-8059 TCGA-BR-8060 TCGA-BR-8080 TCGA-BR-8081 
        0.16         1.08         0.82         1.32         0.49         0.46 
TCGA-BR-8284 TCGA-BR-8285 TCGA-BR-8286 TCGA-BR-8289 TCGA-BR-8291 TCGA-BR-8295 
        0.72         0.26         0.43         0.26         1.18         1.55 
TCGA-BR-8296 TCGA-BR-8297 TCGA-BR-8592 TCGA-BR-A4IU TCGA-BR-A4IV TCGA-BR-A4IY 
        1.48         0.76         0.20         0.59         0.92         0.39 
TCGA-BR-A4IZ TCGA-BR-A4J2 TCGA-BR-A4J4 TCGA-BR-A4J5 TCGA-BR-A4J6 TCGA-BR-A4J9 
        0.79         0.79         0.53         0.43         0.13         0.10 
TCGA-BR-A4QI TCGA-BR-A4QL TCGA-CD-5798 TCGA-CD-5801 TCGA-CD-5802 TCGA-CD-5803 
        0.49         2.24         0.82         0.49         0.30         0.07 
TCGA-CG-4301 TCGA-CG-4304 TCGA-CG-4306 TCGA-CG-4437 TCGA-CG-4438 TCGA-CG-4440 
        3.02        27.02         1.02         8.05        54.05         4.01 
TCGA-CG-4441 TCGA-CG-4443 TCGA-CG-4444 TCGA-CG-4449 TCGA-CG-4455 TCGA-CG-4460 
       14.01        29.98        47.05        19.07        12.03        21.99 
TCGA-CG-4462 TCGA-CG-4465 TCGA-CG-4466 TCGA-CG-4474 TCGA-CG-4477 TCGA-CG-5716 
        1.02         8.98        18.94         1.02         1.02         1.02 
TCGA-CG-5717 TCGA-CG-5718 TCGA-CG-5719 TCGA-CG-5720 TCGA-CG-5721 TCGA-CG-5722 
        6.94         1.02         1.02         0.99         5.98         0.95 
TCGA-CG-5723 TCGA-CG-5724 TCGA-CG-5725 TCGA-CG-5726 TCGA-CG-5727 TCGA-CG-5728 
       70.06        12.03        15.02        28.96        31.04        65.10 
TCGA-CG-5733 TCGA-CG-5734 TCGA-D7-5578 TCGA-D7-5579 TCGA-D7-6519 TCGA-D7-6520 
       21.07         7.99         3.58         4.54        15.65         9.63 
TCGA-D7-6521 TCGA-D7-6522 TCGA-D7-6524 TCGA-D7-6525 TCGA-D7-6528 TCGA-D7-6815 
        8.19         6.90         0.69         5.95         1.68         3.65 
TCGA-D7-6817 TCGA-D7-6818 TCGA-D7-6822 TCGA-EQ-8122 TCGA-F1-6177 TCGA-F1-6874 
        4.70         4.04         4.27         7.79         6.54         2.01 
TCGA-FP-7735 TCGA-FP-7916 TCGA-FP-7998 TCGA-FP-8099 TCGA-FP-8209 TCGA-FP-8210 
        0.39         3.02         3.58         1.02        59.05         5.03 
TCGA-FP-8631 TCGA-HJ-7597 TCGA-IN-7806 TCGA-IN-7808 TCGA-IP-7968 
        0.56        26.43         6.87         3.55         2.53 

      13Q GAIN CNV 13Q GAIN WILD-TYPE 
              0.10               0.07 
      13Q GAIN CNV 13Q GAIN WILD-TYPE 
             72.23              70.06 
      13Q GAIN CNV 13Q GAIN WILD-TYPE 
             1.595              1.220 
[1] "0.1 - 72.2 (1.6)" "0.1 - 70.1 (1.2)"
        TCGA-B7-5816         TCGA-B7-5818         TCGA-BR-6452 
"13Q GAIN WILD-TYPE"       "13Q GAIN CNV" "13Q GAIN WILD-TYPE" 
        TCGA-BR-6455         TCGA-BR-6457         TCGA-BR-6458 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-BR-6563         TCGA-BR-6564         TCGA-BR-6565 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE"       "13Q GAIN CNV" 
        TCGA-BR-6566         TCGA-BR-6705         TCGA-BR-6706 
"13Q GAIN WILD-TYPE"       "13Q GAIN CNV" "13Q GAIN WILD-TYPE" 
        TCGA-BR-6707         TCGA-BR-6709         TCGA-BR-6710 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-BR-6801         TCGA-BR-6802         TCGA-BR-6803 
      "13Q GAIN CNV" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-BR-6852         TCGA-BR-7196         TCGA-BR-7197 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE"       "13Q GAIN CNV" 
        TCGA-BR-7703         TCGA-BR-7704         TCGA-BR-7707 
"13Q GAIN WILD-TYPE"       "13Q GAIN CNV" "13Q GAIN WILD-TYPE" 
        TCGA-BR-7715         TCGA-BR-7716         TCGA-BR-7717 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE"       "13Q GAIN CNV" 
        TCGA-BR-7722         TCGA-BR-7723         TCGA-BR-7851 
"13Q GAIN WILD-TYPE"       "13Q GAIN CNV" "13Q GAIN WILD-TYPE" 
        TCGA-BR-7901         TCGA-BR-7957         TCGA-BR-7958 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-BR-7959         TCGA-BR-8059         TCGA-BR-8060 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-BR-8077         TCGA-BR-8078         TCGA-BR-8080 
      "13Q GAIN CNV"       "13Q GAIN CNV" "13Q GAIN WILD-TYPE" 
        TCGA-BR-8081         TCGA-BR-8284         TCGA-BR-8285 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-BR-8286         TCGA-BR-8289         TCGA-BR-8291 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-BR-8295         TCGA-BR-8296         TCGA-BR-8297 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-BR-8592         TCGA-BR-A4IU         TCGA-BR-A4IV 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-BR-A4IY         TCGA-BR-A4IZ         TCGA-BR-A4J1 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE"       "13Q GAIN CNV" 
        TCGA-BR-A4J2         TCGA-BR-A4J4         TCGA-BR-A4J5 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-BR-A4J6         TCGA-BR-A4J8         TCGA-BR-A4J9 
"13Q GAIN WILD-TYPE"       "13Q GAIN CNV" "13Q GAIN WILD-TYPE" 
        TCGA-BR-A4PF         TCGA-BR-A4QI         TCGA-BR-A4QL 
      "13Q GAIN CNV" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-CD-5798         TCGA-CD-5799         TCGA-CD-5800 
"13Q GAIN WILD-TYPE"       "13Q GAIN CNV"       "13Q GAIN CNV" 
        TCGA-CD-5801         TCGA-CD-5802         TCGA-CD-5803 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-CG-4300         TCGA-CG-4301         TCGA-CG-4304 
      "13Q GAIN CNV" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-CG-4305         TCGA-CG-4306         TCGA-CG-4436 
      "13Q GAIN CNV" "13Q GAIN WILD-TYPE"       "13Q GAIN CNV" 
        TCGA-CG-4437         TCGA-CG-4438         TCGA-CG-4440 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-CG-4441         TCGA-CG-4443         TCGA-CG-4444 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-CG-4449         TCGA-CG-4455         TCGA-CG-4460 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-CG-4462         TCGA-CG-4465         TCGA-CG-4466 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-CG-4469         TCGA-CG-4472         TCGA-CG-4474 
      "13Q GAIN CNV"       "13Q GAIN CNV" "13Q GAIN WILD-TYPE" 
        TCGA-CG-4477         TCGA-CG-5716         TCGA-CG-5717 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-CG-5718         TCGA-CG-5719         TCGA-CG-5720 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-CG-5721         TCGA-CG-5722         TCGA-CG-5723 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-CG-5724         TCGA-CG-5725         TCGA-CG-5726 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-CG-5727         TCGA-CG-5728         TCGA-CG-5730 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE"       "13Q GAIN CNV" 
        TCGA-CG-5732         TCGA-CG-5733         TCGA-CG-5734 
      "13Q GAIN CNV" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-D7-5577         TCGA-D7-5578         TCGA-D7-5579 
      "13Q GAIN CNV" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-D7-6518         TCGA-D7-6519         TCGA-D7-6520 
      "13Q GAIN CNV" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-D7-6521         TCGA-D7-6522         TCGA-D7-6524 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-D7-6525         TCGA-D7-6526         TCGA-D7-6527 
"13Q GAIN WILD-TYPE"       "13Q GAIN CNV"       "13Q GAIN CNV" 
        TCGA-D7-6528         TCGA-D7-6815         TCGA-D7-6817 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-D7-6818         TCGA-D7-6820         TCGA-D7-6822 
"13Q GAIN WILD-TYPE"       "13Q GAIN CNV" "13Q GAIN WILD-TYPE" 
        TCGA-EQ-5647         TCGA-EQ-8122         TCGA-F1-6177 
      "13Q GAIN CNV" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-F1-6874         TCGA-F1-6875         TCGA-FP-7735 
"13Q GAIN WILD-TYPE"       "13Q GAIN CNV" "13Q GAIN WILD-TYPE" 
        TCGA-FP-7829         TCGA-FP-7916         TCGA-FP-7998 
      "13Q GAIN CNV" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-FP-8099         TCGA-FP-8209         TCGA-FP-8210 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-FP-8631         TCGA-HJ-7597         TCGA-IN-7806 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-IN-7808         TCGA-IP-7968 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-B7-5816         TCGA-B7-5818         TCGA-BR-6452 
"13Q GAIN WILD-TYPE"       "13Q GAIN CNV" "13Q GAIN WILD-TYPE" 
        TCGA-BR-6455         TCGA-BR-6457         TCGA-BR-6458 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-BR-6563         TCGA-BR-6564         TCGA-BR-6565 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE"       "13Q GAIN CNV" 
        TCGA-BR-6566         TCGA-BR-6705         TCGA-BR-6706 
"13Q GAIN WILD-TYPE"       "13Q GAIN CNV" "13Q GAIN WILD-TYPE" 
        TCGA-BR-6707         TCGA-BR-6709         TCGA-BR-6710 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-BR-6801         TCGA-BR-6802         TCGA-BR-6803 
      "13Q GAIN CNV" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-BR-6852         TCGA-BR-7196         TCGA-BR-7197 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE"       "13Q GAIN CNV" 
        TCGA-BR-7703         TCGA-BR-7704         TCGA-BR-7707 
"13Q GAIN WILD-TYPE"       "13Q GAIN CNV" "13Q GAIN WILD-TYPE" 
        TCGA-BR-7715         TCGA-BR-7716         TCGA-BR-7717 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE"       "13Q GAIN CNV" 
        TCGA-BR-7722         TCGA-BR-7723         TCGA-BR-7851 
"13Q GAIN WILD-TYPE"       "13Q GAIN CNV" "13Q GAIN WILD-TYPE" 
        TCGA-BR-7901         TCGA-BR-7957         TCGA-BR-7958 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-BR-7959         TCGA-BR-8059         TCGA-BR-8060 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-BR-8077         TCGA-BR-8078         TCGA-BR-8080 
      "13Q GAIN CNV"       "13Q GAIN CNV" "13Q GAIN WILD-TYPE" 
        TCGA-BR-8081         TCGA-BR-8284         TCGA-BR-8285 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-BR-8286         TCGA-BR-8289         TCGA-BR-8291 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-BR-8295         TCGA-BR-8296         TCGA-BR-8297 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-BR-8592         TCGA-BR-A4IU         TCGA-BR-A4IV 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-BR-A4IY         TCGA-BR-A4IZ         TCGA-BR-A4J1 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE"       "13Q GAIN CNV" 
        TCGA-BR-A4J2         TCGA-BR-A4J4         TCGA-BR-A4J5 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-BR-A4J6         TCGA-BR-A4J8         TCGA-BR-A4J9 
"13Q GAIN WILD-TYPE"       "13Q GAIN CNV" "13Q GAIN WILD-TYPE" 
        TCGA-BR-A4PF         TCGA-BR-A4QI         TCGA-BR-A4QL 
      "13Q GAIN CNV" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-CD-5798         TCGA-CD-5799         TCGA-CD-5800 
"13Q GAIN WILD-TYPE"       "13Q GAIN CNV"       "13Q GAIN CNV" 
        TCGA-CD-5801         TCGA-CD-5802         TCGA-CD-5803 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-CG-4300         TCGA-CG-4301         TCGA-CG-4304 
      "13Q GAIN CNV" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-CG-4305         TCGA-CG-4306         TCGA-CG-4436 
      "13Q GAIN CNV" "13Q GAIN WILD-TYPE"       "13Q GAIN CNV" 
        TCGA-CG-4437         TCGA-CG-4438         TCGA-CG-4440 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-CG-4441         TCGA-CG-4443         TCGA-CG-4444 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-CG-4449         TCGA-CG-4455         TCGA-CG-4460 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-CG-4462         TCGA-CG-4465         TCGA-CG-4466 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-CG-4469         TCGA-CG-4472         TCGA-CG-4474 
      "13Q GAIN CNV"       "13Q GAIN CNV" "13Q GAIN WILD-TYPE" 
        TCGA-CG-4477         TCGA-CG-5716         TCGA-CG-5717 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-CG-5718         TCGA-CG-5719         TCGA-CG-5720 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-CG-5721         TCGA-CG-5722         TCGA-CG-5723 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-CG-5724         TCGA-CG-5725         TCGA-CG-5726 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-CG-5727         TCGA-CG-5728         TCGA-CG-5730 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE"       "13Q GAIN CNV" 
        TCGA-CG-5732         TCGA-CG-5733         TCGA-CG-5734 
      "13Q GAIN CNV" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-D7-5577         TCGA-D7-5578         TCGA-D7-5579 
      "13Q GAIN CNV" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-D7-6518         TCGA-D7-6519         TCGA-D7-6520 
      "13Q GAIN CNV" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-D7-6521         TCGA-D7-6522         TCGA-D7-6524 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-D7-6525         TCGA-D7-6526         TCGA-D7-6527 
"13Q GAIN WILD-TYPE"       "13Q GAIN CNV"       "13Q GAIN CNV" 
        TCGA-D7-6528         TCGA-D7-6815         TCGA-D7-6817 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-D7-6818         TCGA-D7-6820         TCGA-D7-6822 
"13Q GAIN WILD-TYPE"       "13Q GAIN CNV" "13Q GAIN WILD-TYPE" 
        TCGA-EQ-5647         TCGA-EQ-8122         TCGA-F1-6177 
      "13Q GAIN CNV" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-F1-6874         TCGA-F1-6875         TCGA-FP-7735 
"13Q GAIN WILD-TYPE"       "13Q GAIN CNV" "13Q GAIN WILD-TYPE" 
        TCGA-FP-7829         TCGA-FP-7916         TCGA-FP-7998 
      "13Q GAIN CNV" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-FP-8099         TCGA-FP-8209         TCGA-FP-8210 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-FP-8631         TCGA-HJ-7597         TCGA-IN-7806 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-IN-7808         TCGA-IP-7968 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-B7-5816         TCGA-B7-5818         TCGA-BR-6452 
"13Q GAIN WILD-TYPE"       "13Q GAIN CNV" "13Q GAIN WILD-TYPE" 
        TCGA-BR-6455         TCGA-BR-6457         TCGA-BR-6458 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-BR-6563         TCGA-BR-6564         TCGA-BR-6565 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE"       "13Q GAIN CNV" 
        TCGA-BR-6566         TCGA-BR-6705         TCGA-BR-6706 
"13Q GAIN WILD-TYPE"       "13Q GAIN CNV" "13Q GAIN WILD-TYPE" 
        TCGA-BR-6707         TCGA-BR-6709         TCGA-BR-6710 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-BR-6801         TCGA-BR-6802         TCGA-BR-6803 
      "13Q GAIN CNV" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-BR-6852         TCGA-BR-7196         TCGA-BR-7197 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE"       "13Q GAIN CNV" 
        TCGA-BR-7703         TCGA-BR-7704         TCGA-BR-7707 
"13Q GAIN WILD-TYPE"       "13Q GAIN CNV" "13Q GAIN WILD-TYPE" 
        TCGA-BR-7715         TCGA-BR-7716         TCGA-BR-7717 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE"       "13Q GAIN CNV" 
        TCGA-BR-7722         TCGA-BR-7723         TCGA-BR-7851 
"13Q GAIN WILD-TYPE"       "13Q GAIN CNV" "13Q GAIN WILD-TYPE" 
        TCGA-BR-7901         TCGA-BR-7957         TCGA-BR-7958 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-BR-7959         TCGA-BR-8059         TCGA-BR-8060 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-BR-8077         TCGA-BR-8078         TCGA-BR-8080 
      "13Q GAIN CNV"       "13Q GAIN CNV" "13Q GAIN WILD-TYPE" 
        TCGA-BR-8081         TCGA-BR-8284         TCGA-BR-8285 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-BR-8286         TCGA-BR-8289         TCGA-BR-8291 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-BR-8295         TCGA-BR-8296         TCGA-BR-8297 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-BR-8592         TCGA-BR-A4IU         TCGA-BR-A4IV 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-BR-A4IY         TCGA-BR-A4IZ         TCGA-BR-A4J1 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE"       "13Q GAIN CNV" 
        TCGA-BR-A4J2         TCGA-BR-A4J4         TCGA-BR-A4J5 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-BR-A4J6         TCGA-BR-A4J8         TCGA-BR-A4J9 
"13Q GAIN WILD-TYPE"       "13Q GAIN CNV" "13Q GAIN WILD-TYPE" 
        TCGA-BR-A4PF         TCGA-BR-A4QI         TCGA-BR-A4QL 
      "13Q GAIN CNV" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-CD-5798         TCGA-CD-5799         TCGA-CD-5800 
"13Q GAIN WILD-TYPE"       "13Q GAIN CNV"       "13Q GAIN CNV" 
        TCGA-CD-5801         TCGA-CD-5802         TCGA-CD-5803 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-CG-4300         TCGA-CG-4301         TCGA-CG-4304 
      "13Q GAIN CNV" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-CG-4305         TCGA-CG-4306         TCGA-CG-4436 
      "13Q GAIN CNV" "13Q GAIN WILD-TYPE"       "13Q GAIN CNV" 
        TCGA-CG-4437         TCGA-CG-4438         TCGA-CG-4440 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-CG-4441         TCGA-CG-4443         TCGA-CG-4444 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-CG-4449         TCGA-CG-4455         TCGA-CG-4460 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-CG-4462         TCGA-CG-4465         TCGA-CG-4466 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-CG-4469         TCGA-CG-4472         TCGA-CG-4474 
      "13Q GAIN CNV"       "13Q GAIN CNV" "13Q GAIN WILD-TYPE" 
        TCGA-CG-4477         TCGA-CG-5716         TCGA-CG-5717 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-CG-5718         TCGA-CG-5719         TCGA-CG-5720 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-CG-5721         TCGA-CG-5722         TCGA-CG-5723 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-CG-5724         TCGA-CG-5725         TCGA-CG-5726 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-CG-5727         TCGA-CG-5728         TCGA-CG-5730 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE"       "13Q GAIN CNV" 
        TCGA-CG-5732         TCGA-CG-5733         TCGA-CG-5734 
      "13Q GAIN CNV" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-D7-5577         TCGA-D7-5578         TCGA-D7-5579 
      "13Q GAIN CNV" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-D7-6518         TCGA-D7-6519         TCGA-D7-6520 
      "13Q GAIN CNV" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-D7-6521         TCGA-D7-6522         TCGA-D7-6524 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-D7-6525         TCGA-D7-6526         TCGA-D7-6527 
"13Q GAIN WILD-TYPE"       "13Q GAIN CNV"       "13Q GAIN CNV" 
        TCGA-D7-6528         TCGA-D7-6815         TCGA-D7-6817 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-D7-6818         TCGA-D7-6820         TCGA-D7-6822 
"13Q GAIN WILD-TYPE"       "13Q GAIN CNV" "13Q GAIN WILD-TYPE" 
        TCGA-EQ-5647         TCGA-EQ-8122         TCGA-F1-6177 
      "13Q GAIN CNV" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-F1-6874         TCGA-F1-6875         TCGA-FP-7735 
"13Q GAIN WILD-TYPE"       "13Q GAIN CNV" "13Q GAIN WILD-TYPE" 
        TCGA-FP-7829         TCGA-FP-7916         TCGA-FP-7998 
      "13Q GAIN CNV" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-FP-8099         TCGA-FP-8209         TCGA-FP-8210 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-FP-8631         TCGA-HJ-7597         TCGA-IN-7806 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-IN-7808         TCGA-IP-7968 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
[1] "hr=" "1.5"
D24V2, continuous
D24V3, binary
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  13Q GAIN CNV         13   23
  13Q GAIN WILD-TYPE   59   85
        clus
vv       13Q GAIN CNV 13Q GAIN WILD-TYPE
  FEMALE           13                 59
  MALE             23                 85
                    vv
clus                 STOMACH  ADENOCARCINOMA  DIFFUSE TYPE
  13Q GAIN CNV                                           0
  13Q GAIN WILD-TYPE                                    10
                    vv
clus                 STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  13Q GAIN CNV                                                            4
  13Q GAIN WILD-TYPE                                                     12
                    vv
clus                 STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  13Q GAIN CNV                                                                       1
  13Q GAIN WILD-TYPE                                                                 7
                    vv
clus                 STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE
  13Q GAIN CNV                                                              0
  13Q GAIN WILD-TYPE                                                        3
                    vv
clus                 STOMACH ADENOCARCINOMA  SIGNET RING TYPE
  13Q GAIN CNV                                              0
  13Q GAIN WILD-TYPE                                        1
                    vv
clus                 STOMACH ADENOCARCINOMA - DIFFUSE TYPE
  13Q GAIN CNV                                           3
  13Q GAIN WILD-TYPE                                    13
                    vv
clus                 STOMACH ADENOCARCINOMA - NOT OTHERWISE SPECIFIED (NOS)
  13Q GAIN CNV                                                           14
  13Q GAIN WILD-TYPE                                                     59
                    vv
clus                 STOMACH INTESTINAL ADENOCARCINOMA - MUCINOUS TYPE
  13Q GAIN CNV                                                       1
  13Q GAIN WILD-TYPE                                                 6
                    vv
clus                 STOMACH INTESTINAL ADENOCARCINOMA - PAPILLARY TYPE
  13Q GAIN CNV                                                        2
  13Q GAIN WILD-TYPE                                                  1
                    vv
clus                 STOMACH INTESTINAL ADENOCARCINOMA - TUBULAR TYPE
  13Q GAIN CNV                                                      3
  13Q GAIN WILD-TYPE                                                7
                    vv
clus                 STOMACH INTESTINAL ADENOCARCINOMA - TYPE NOT OTHERWISE SPECIFIED (NOS)
  13Q GAIN CNV                                                                            7
  13Q GAIN WILD-TYPE                                                                     21
D24V4, multiclass
                    vv
clus                 T1 T2 T3 T4
  13Q GAIN CNV        1 13 11  5
  13Q GAIN WILD-TYPE  5 39 45 13
D24V5, multiclass
    clus
vv   13Q GAIN CNV 13Q GAIN WILD-TYPE
  T1            1                  5
  T2           13                 39
  T3           11                 45
  T4            5                 13
                    vv
clus                 N0 N1 N2 N3
  13Q GAIN CNV        9 10  4  6
  13Q GAIN WILD-TYPE 35 39 19  9
D24V6, multiclass
    clus
vv   13Q GAIN CNV 13Q GAIN WILD-TYPE
  N0            9                 35
  N1           10                 39
  N2            4                 19
  N3            6                  9
                    vv
clus                 M0 M1 MX
  13Q GAIN CNV       28  2  1
  13Q GAIN WILD-TYPE 90 14  7
D24V7, multiclass
    clus
vv   13Q GAIN CNV 13Q GAIN WILD-TYPE
  M0           28                 90
  M1            2                 14
  MX            1                  7
                    vv
clus                  I II III IV
  13Q GAIN CNV        4  9   8  7
  13Q GAIN WILD-TYPE 20 28  31 19
D24V8, multiclass
     clus
vv    13Q GAIN CNV 13Q GAIN WILD-TYPE
  I              4                 20
  II             9                 28
  III            8                 31
  IV             7                 19
D24V9, binary
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  13Q GAIN CNV          1   35
  13Q GAIN WILD-TYPE    4  140
     clus
vv    13Q GAIN CNV 13Q GAIN WILD-TYPE
  NO             1                  4
  YES           35                140
                    vv
clus                 R0 R1 R2 RX
  13Q GAIN CNV       26  2  2  4
  13Q GAIN WILD-TYPE 99  5 10 21
D24V10, multiclass
    clus
vv   13Q GAIN CNV 13Q GAIN WILD-TYPE
  R0           26                 99
  R1            2                  5
  R2            2                 10
  RX            4                 21
D24V11, continuous

Clustering(25) Variable = 14q gain
D25V1, survival
                    sevent
clus2                  0   1
  14Q GAIN CNV         1   2
  14Q GAIN WILD-TYPE 123  17
      14Q GAIN CNV 14Q GAIN WILD-TYPE 
                 3                140 
      14Q GAIN CNV 14Q GAIN WILD-TYPE 
                 2                 17 
$`14Q GAIN CNV`
TCGA-BR-8295 TCGA-CG-4460 TCGA-EQ-5647 
        1.55        21.99         0.62 

$`14Q GAIN WILD-TYPE`
TCGA-B7-5816 TCGA-B7-5818 TCGA-BR-6452 TCGA-BR-6455 TCGA-BR-6457 TCGA-BR-6458 
        5.62         0.10         0.95         1.41         1.35         1.35 
TCGA-BR-6563 TCGA-BR-6564 TCGA-BR-6565 TCGA-BR-6566 TCGA-BR-6705 TCGA-BR-6706 
        0.85         0.82         0.62         0.62         1.71         2.17 
TCGA-BR-6707 TCGA-BR-6709 TCGA-BR-6710 TCGA-BR-6801 TCGA-BR-6802 TCGA-BR-6803 
        0.99         1.22         0.66         1.12         0.76         0.66 
TCGA-BR-6852 TCGA-BR-7196 TCGA-BR-7197 TCGA-BR-7703 TCGA-BR-7704 TCGA-BR-7707 
        0.26         1.22         1.48         0.46         1.25         0.13 
TCGA-BR-7715 TCGA-BR-7716 TCGA-BR-7717 TCGA-BR-7722 TCGA-BR-7723 TCGA-BR-7851 
        1.05         0.82         0.69         0.16         4.54         0.99 
TCGA-BR-7901 TCGA-BR-7957 TCGA-BR-7958 TCGA-BR-7959 TCGA-BR-8059 TCGA-BR-8060 
        0.95         0.69         0.16         1.08         0.82         1.32 
TCGA-BR-8077 TCGA-BR-8078 TCGA-BR-8080 TCGA-BR-8081 TCGA-BR-8284 TCGA-BR-8285 
        0.69         0.95         0.49         0.46         0.72         0.26 
TCGA-BR-8286 TCGA-BR-8289 TCGA-BR-8291 TCGA-BR-8296 TCGA-BR-8297 TCGA-BR-8592 
        0.43         0.26         1.18         1.48         0.76         0.20 
TCGA-BR-A4IU TCGA-BR-A4IV TCGA-BR-A4IY TCGA-BR-A4IZ TCGA-BR-A4J1 TCGA-BR-A4J2 
        0.59         0.92         0.39         0.79         0.72         0.79 
TCGA-BR-A4J4 TCGA-BR-A4J5 TCGA-BR-A4J6 TCGA-BR-A4J8 TCGA-BR-A4J9 TCGA-BR-A4PF 
        0.53         0.43         0.13         0.23         0.10         0.72 
TCGA-BR-A4QI TCGA-BR-A4QL TCGA-CD-5798 TCGA-CD-5799 TCGA-CD-5800 TCGA-CD-5801 
        0.49         2.24         0.82         0.69         0.36         0.49 
TCGA-CD-5802 TCGA-CD-5803 TCGA-CG-4300 TCGA-CG-4301 TCGA-CG-4304 TCGA-CG-4305 
        0.30         0.07        20.02         3.02        27.02        15.95 
TCGA-CG-4306 TCGA-CG-4436 TCGA-CG-4437 TCGA-CG-4438 TCGA-CG-4440 TCGA-CG-4441 
        1.02        52.96         8.05        54.05         4.01        14.01 
TCGA-CG-4443 TCGA-CG-4444 TCGA-CG-4449 TCGA-CG-4455 TCGA-CG-4462 TCGA-CG-4465 
       29.98        47.05        19.07        12.03         1.02         8.98 
TCGA-CG-4466 TCGA-CG-4469 TCGA-CG-4472 TCGA-CG-4474 TCGA-CG-4477 TCGA-CG-5716 
       18.94         7.07        12.00         1.02         1.02         1.02 
TCGA-CG-5717 TCGA-CG-5718 TCGA-CG-5719 TCGA-CG-5720 TCGA-CG-5721 TCGA-CG-5722 
        6.94         1.02         1.02         0.99         5.98         0.95 
TCGA-CG-5723 TCGA-CG-5724 TCGA-CG-5725 TCGA-CG-5726 TCGA-CG-5727 TCGA-CG-5728 
       70.06        12.03        15.02        28.96        31.04        65.10 
TCGA-CG-5730 TCGA-CG-5732 TCGA-CG-5733 TCGA-CG-5734 TCGA-D7-5577 TCGA-D7-5578 
        4.01        55.04        21.07         7.99         8.65         3.58 
TCGA-D7-5579 TCGA-D7-6518 TCGA-D7-6519 TCGA-D7-6520 TCGA-D7-6521 TCGA-D7-6522 
        4.54         9.80        15.65         9.63         8.19         6.90 
TCGA-D7-6524 TCGA-D7-6525 TCGA-D7-6526 TCGA-D7-6527 TCGA-D7-6528 TCGA-D7-6815 
        0.69         5.95         6.61         4.14         1.68         3.65 
TCGA-D7-6817 TCGA-D7-6818 TCGA-D7-6820 TCGA-D7-6822 TCGA-EQ-8122 TCGA-F1-6177 
        4.70         4.04         2.93         4.27         7.79         6.54 
TCGA-F1-6874 TCGA-F1-6875 TCGA-FP-7735 TCGA-FP-7829 TCGA-FP-7916 TCGA-FP-7998 
        2.01        72.23         0.39         0.20         3.02         3.58 
TCGA-FP-8099 TCGA-FP-8209 TCGA-FP-8210 TCGA-FP-8631 TCGA-HJ-7597 TCGA-IN-7806 
        1.02        59.05         5.03         0.56        26.43         6.87 
TCGA-IN-7808 TCGA-IP-7968 
        3.55         2.53 

      14Q GAIN CNV 14Q GAIN WILD-TYPE 
              0.62               0.07 
      14Q GAIN CNV 14Q GAIN WILD-TYPE 
             21.99              72.23 
      14Q GAIN CNV 14Q GAIN WILD-TYPE 
             1.550              1.235 
[1] "0.6 - 22.0 (1.6)" "0.1 - 72.2 (1.2)"
        TCGA-B7-5816         TCGA-B7-5818         TCGA-BR-6452 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-BR-6455         TCGA-BR-6457         TCGA-BR-6458 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-BR-6563         TCGA-BR-6564         TCGA-BR-6565 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-BR-6566         TCGA-BR-6705         TCGA-BR-6706 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-BR-6707         TCGA-BR-6709         TCGA-BR-6710 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-BR-6801         TCGA-BR-6802         TCGA-BR-6803 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-BR-6852         TCGA-BR-7196         TCGA-BR-7197 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-BR-7703         TCGA-BR-7704         TCGA-BR-7707 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-BR-7715         TCGA-BR-7716         TCGA-BR-7717 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-BR-7722         TCGA-BR-7723         TCGA-BR-7851 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-BR-7901         TCGA-BR-7957         TCGA-BR-7958 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-BR-7959         TCGA-BR-8059         TCGA-BR-8060 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-BR-8077         TCGA-BR-8078         TCGA-BR-8080 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-BR-8081         TCGA-BR-8284         TCGA-BR-8285 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-BR-8286         TCGA-BR-8289         TCGA-BR-8291 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-BR-8295         TCGA-BR-8296         TCGA-BR-8297 
      "14Q GAIN CNV" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-BR-8592         TCGA-BR-A4IU         TCGA-BR-A4IV 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-BR-A4IY         TCGA-BR-A4IZ         TCGA-BR-A4J1 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-BR-A4J2         TCGA-BR-A4J4         TCGA-BR-A4J5 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-BR-A4J6         TCGA-BR-A4J8         TCGA-BR-A4J9 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-BR-A4PF         TCGA-BR-A4QI         TCGA-BR-A4QL 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-CD-5798         TCGA-CD-5799         TCGA-CD-5800 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-CD-5801         TCGA-CD-5802         TCGA-CD-5803 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-CG-4300         TCGA-CG-4301         TCGA-CG-4304 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-CG-4305         TCGA-CG-4306         TCGA-CG-4436 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-CG-4437         TCGA-CG-4438         TCGA-CG-4440 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-CG-4441         TCGA-CG-4443         TCGA-CG-4444 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-CG-4449         TCGA-CG-4455         TCGA-CG-4460 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE"       "14Q GAIN CNV" 
        TCGA-CG-4462         TCGA-CG-4465         TCGA-CG-4466 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-CG-4469         TCGA-CG-4472         TCGA-CG-4474 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-CG-4477         TCGA-CG-5716         TCGA-CG-5717 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-CG-5718         TCGA-CG-5719         TCGA-CG-5720 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-CG-5721         TCGA-CG-5722         TCGA-CG-5723 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-CG-5724         TCGA-CG-5725         TCGA-CG-5726 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-CG-5727         TCGA-CG-5728         TCGA-CG-5730 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-CG-5732         TCGA-CG-5733         TCGA-CG-5734 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-D7-5577         TCGA-D7-5578         TCGA-D7-5579 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-D7-6518         TCGA-D7-6519         TCGA-D7-6520 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-D7-6521         TCGA-D7-6522         TCGA-D7-6524 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-D7-6525         TCGA-D7-6526         TCGA-D7-6527 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-D7-6528         TCGA-D7-6815         TCGA-D7-6817 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-D7-6818         TCGA-D7-6820         TCGA-D7-6822 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-EQ-5647         TCGA-EQ-8122         TCGA-F1-6177 
      "14Q GAIN CNV" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-F1-6874         TCGA-F1-6875         TCGA-FP-7735 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-FP-7829         TCGA-FP-7916         TCGA-FP-7998 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-FP-8099         TCGA-FP-8209         TCGA-FP-8210 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-FP-8631         TCGA-HJ-7597         TCGA-IN-7806 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-IN-7808         TCGA-IP-7968 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-B7-5816         TCGA-B7-5818         TCGA-BR-6452 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-BR-6455         TCGA-BR-6457         TCGA-BR-6458 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-BR-6563         TCGA-BR-6564         TCGA-BR-6565 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-BR-6566         TCGA-BR-6705         TCGA-BR-6706 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-BR-6707         TCGA-BR-6709         TCGA-BR-6710 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-BR-6801         TCGA-BR-6802         TCGA-BR-6803 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-BR-6852         TCGA-BR-7196         TCGA-BR-7197 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-BR-7703         TCGA-BR-7704         TCGA-BR-7707 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-BR-7715         TCGA-BR-7716         TCGA-BR-7717 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-BR-7722         TCGA-BR-7723         TCGA-BR-7851 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-BR-7901         TCGA-BR-7957         TCGA-BR-7958 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-BR-7959         TCGA-BR-8059         TCGA-BR-8060 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-BR-8077         TCGA-BR-8078         TCGA-BR-8080 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-BR-8081         TCGA-BR-8284         TCGA-BR-8285 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-BR-8286         TCGA-BR-8289         TCGA-BR-8291 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-BR-8295         TCGA-BR-8296         TCGA-BR-8297 
      "14Q GAIN CNV" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-BR-8592         TCGA-BR-A4IU         TCGA-BR-A4IV 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-BR-A4IY         TCGA-BR-A4IZ         TCGA-BR-A4J1 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-BR-A4J2         TCGA-BR-A4J4         TCGA-BR-A4J5 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-BR-A4J6         TCGA-BR-A4J8         TCGA-BR-A4J9 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-BR-A4PF         TCGA-BR-A4QI         TCGA-BR-A4QL 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-CD-5798         TCGA-CD-5799         TCGA-CD-5800 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-CD-5801         TCGA-CD-5802         TCGA-CD-5803 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-CG-4300         TCGA-CG-4301         TCGA-CG-4304 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-CG-4305         TCGA-CG-4306         TCGA-CG-4436 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-CG-4437         TCGA-CG-4438         TCGA-CG-4440 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-CG-4441         TCGA-CG-4443         TCGA-CG-4444 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-CG-4449         TCGA-CG-4455         TCGA-CG-4460 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE"       "14Q GAIN CNV" 
        TCGA-CG-4462         TCGA-CG-4465         TCGA-CG-4466 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-CG-4469         TCGA-CG-4472         TCGA-CG-4474 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-CG-4477         TCGA-CG-5716         TCGA-CG-5717 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-CG-5718         TCGA-CG-5719         TCGA-CG-5720 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-CG-5721         TCGA-CG-5722         TCGA-CG-5723 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-CG-5724         TCGA-CG-5725         TCGA-CG-5726 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-CG-5727         TCGA-CG-5728         TCGA-CG-5730 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-CG-5732         TCGA-CG-5733         TCGA-CG-5734 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-D7-5577         TCGA-D7-5578         TCGA-D7-5579 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-D7-6518         TCGA-D7-6519         TCGA-D7-6520 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-D7-6521         TCGA-D7-6522         TCGA-D7-6524 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-D7-6525         TCGA-D7-6526         TCGA-D7-6527 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-D7-6528         TCGA-D7-6815         TCGA-D7-6817 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-D7-6818         TCGA-D7-6820         TCGA-D7-6822 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-EQ-5647         TCGA-EQ-8122         TCGA-F1-6177 
      "14Q GAIN CNV" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-F1-6874         TCGA-F1-6875         TCGA-FP-7735 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-FP-7829         TCGA-FP-7916         TCGA-FP-7998 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-FP-8099         TCGA-FP-8209         TCGA-FP-8210 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-FP-8631         TCGA-HJ-7597         TCGA-IN-7806 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-IN-7808         TCGA-IP-7968 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-B7-5816         TCGA-B7-5818         TCGA-BR-6452 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-BR-6455         TCGA-BR-6457         TCGA-BR-6458 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-BR-6563         TCGA-BR-6564         TCGA-BR-6565 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-BR-6566         TCGA-BR-6705         TCGA-BR-6706 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-BR-6707         TCGA-BR-6709         TCGA-BR-6710 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-BR-6801         TCGA-BR-6802         TCGA-BR-6803 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-BR-6852         TCGA-BR-7196         TCGA-BR-7197 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-BR-7703         TCGA-BR-7704         TCGA-BR-7707 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-BR-7715         TCGA-BR-7716         TCGA-BR-7717 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-BR-7722         TCGA-BR-7723         TCGA-BR-7851 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-BR-7901         TCGA-BR-7957         TCGA-BR-7958 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-BR-7959         TCGA-BR-8059         TCGA-BR-8060 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-BR-8077         TCGA-BR-8078         TCGA-BR-8080 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-BR-8081         TCGA-BR-8284         TCGA-BR-8285 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-BR-8286         TCGA-BR-8289         TCGA-BR-8291 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-BR-8295         TCGA-BR-8296         TCGA-BR-8297 
      "14Q GAIN CNV" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-BR-8592         TCGA-BR-A4IU         TCGA-BR-A4IV 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-BR-A4IY         TCGA-BR-A4IZ         TCGA-BR-A4J1 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-BR-A4J2         TCGA-BR-A4J4         TCGA-BR-A4J5 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-BR-A4J6         TCGA-BR-A4J8         TCGA-BR-A4J9 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-BR-A4PF         TCGA-BR-A4QI         TCGA-BR-A4QL 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-CD-5798         TCGA-CD-5799         TCGA-CD-5800 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-CD-5801         TCGA-CD-5802         TCGA-CD-5803 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-CG-4300         TCGA-CG-4301         TCGA-CG-4304 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-CG-4305         TCGA-CG-4306         TCGA-CG-4436 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-CG-4437         TCGA-CG-4438         TCGA-CG-4440 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-CG-4441         TCGA-CG-4443         TCGA-CG-4444 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-CG-4449         TCGA-CG-4455         TCGA-CG-4460 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE"       "14Q GAIN CNV" 
        TCGA-CG-4462         TCGA-CG-4465         TCGA-CG-4466 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-CG-4469         TCGA-CG-4472         TCGA-CG-4474 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-CG-4477         TCGA-CG-5716         TCGA-CG-5717 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-CG-5718         TCGA-CG-5719         TCGA-CG-5720 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-CG-5721         TCGA-CG-5722         TCGA-CG-5723 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-CG-5724         TCGA-CG-5725         TCGA-CG-5726 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-CG-5727         TCGA-CG-5728         TCGA-CG-5730 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-CG-5732         TCGA-CG-5733         TCGA-CG-5734 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-D7-5577         TCGA-D7-5578         TCGA-D7-5579 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-D7-6518         TCGA-D7-6519         TCGA-D7-6520 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-D7-6521         TCGA-D7-6522         TCGA-D7-6524 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-D7-6525         TCGA-D7-6526         TCGA-D7-6527 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-D7-6528         TCGA-D7-6815         TCGA-D7-6817 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-D7-6818         TCGA-D7-6820         TCGA-D7-6822 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-EQ-5647         TCGA-EQ-8122         TCGA-F1-6177 
      "14Q GAIN CNV" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-F1-6874         TCGA-F1-6875         TCGA-FP-7735 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-FP-7829         TCGA-FP-7916         TCGA-FP-7998 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-FP-8099         TCGA-FP-8209         TCGA-FP-8210 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-FP-8631         TCGA-HJ-7597         TCGA-IN-7806 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-IN-7808         TCGA-IP-7968 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
[1] "hr=" "4.3"
D25V2, continuous
D25V3, binary
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  14Q GAIN CNV          3    0
  14Q GAIN WILD-TYPE   69  108
        clus
vv       14Q GAIN CNV 14Q GAIN WILD-TYPE
  FEMALE            3                 69
  MALE              0                108
                    vv
clus                 STOMACH  ADENOCARCINOMA  DIFFUSE TYPE
  14Q GAIN CNV                                           0
  14Q GAIN WILD-TYPE                                    10
                    vv
clus                 STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  14Q GAIN CNV                                                            1
  14Q GAIN WILD-TYPE                                                     15
                    vv
clus                 STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  14Q GAIN CNV                                                                       0
  14Q GAIN WILD-TYPE                                                                 8
                    vv
clus                 STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE
  14Q GAIN CNV                                                              0
  14Q GAIN WILD-TYPE                                                        3
                    vv
clus                 STOMACH ADENOCARCINOMA  SIGNET RING TYPE
  14Q GAIN CNV                                              0
  14Q GAIN WILD-TYPE                                        1
                    vv
clus                 STOMACH ADENOCARCINOMA - DIFFUSE TYPE
  14Q GAIN CNV                                           0
  14Q GAIN WILD-TYPE                                    16
                    vv
clus                 STOMACH ADENOCARCINOMA - NOT OTHERWISE SPECIFIED (NOS)
  14Q GAIN CNV                                                            1
  14Q GAIN WILD-TYPE                                                     72
                    vv
clus                 STOMACH INTESTINAL ADENOCARCINOMA - MUCINOUS TYPE
  14Q GAIN CNV                                                       0
  14Q GAIN WILD-TYPE                                                 7
                    vv
clus                 STOMACH INTESTINAL ADENOCARCINOMA - PAPILLARY TYPE
  14Q GAIN CNV                                                        0
  14Q GAIN WILD-TYPE                                                  3
                    vv
clus                 STOMACH INTESTINAL ADENOCARCINOMA - TUBULAR TYPE
  14Q GAIN CNV                                                      0
  14Q GAIN WILD-TYPE                                               10
                    vv
clus                 STOMACH INTESTINAL ADENOCARCINOMA - TYPE NOT OTHERWISE SPECIFIED (NOS)
  14Q GAIN CNV                                                                            1
  14Q GAIN WILD-TYPE                                                                     27
D25V4, multiclass
                    vv
clus                 T1 T2 T3 T4
  14Q GAIN CNV        0  0  0  2
  14Q GAIN WILD-TYPE  6 52 56 16
D25V5, multiclass
[1] "Remove cluster labels:" "14Q GAIN CNV"          
clus
      14Q GAIN CNV 14Q GAIN WILD-TYPE 
                 2                130 
        TCGA-B7-5816         TCGA-B7-5818         TCGA-BR-4183 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-BR-4184         TCGA-BR-4201         TCGA-BR-4253 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-BR-4255         TCGA-BR-4267         TCGA-BR-4279 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-BR-4280         TCGA-BR-4292         TCGA-BR-4294 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-BR-4357         TCGA-BR-4361         TCGA-BR-4363 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-BR-4368         TCGA-BR-4371         TCGA-BR-6452 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-BR-6453         TCGA-BR-6454         TCGA-BR-6455 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-BR-6456         TCGA-BR-6457         TCGA-BR-6458 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-BR-6563         TCGA-BR-6564         TCGA-BR-6565 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-BR-6566         TCGA-BR-6705         TCGA-BR-6706 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-BR-6707         TCGA-BR-6709         TCGA-BR-6710 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-BR-6801         TCGA-BR-6802         TCGA-BR-6803 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-BR-6852         TCGA-BR-7196         TCGA-BR-7197 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-BR-7703         TCGA-BR-7704         TCGA-BR-7707 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-BR-7715         TCGA-BR-7716         TCGA-BR-7717 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-BR-7722         TCGA-BR-7723         TCGA-BR-7851 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-BR-7901         TCGA-BR-7957         TCGA-CD-5798 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-CD-5799         TCGA-CD-5800         TCGA-CD-5801 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-CD-5802         TCGA-CD-5803         TCGA-CD-5804 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-CG-4300         TCGA-CG-4301         TCGA-CG-4304 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-CG-4305         TCGA-CG-4306         TCGA-CG-4436 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-CG-4437         TCGA-CG-4438         TCGA-CG-4440 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-CG-4441         TCGA-CG-4442         TCGA-CG-4443 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-CG-4444         TCGA-CG-4449         TCGA-CG-4455 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-CG-4462         TCGA-CG-4465         TCGA-CG-4466 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-CG-4469         TCGA-CG-4472         TCGA-CG-4474 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-CG-4475         TCGA-CG-4476         TCGA-CG-4477 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-CG-5716         TCGA-CG-5717         TCGA-CG-5718 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-CG-5719         TCGA-CG-5720         TCGA-CG-5721 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-CG-5722         TCGA-CG-5723         TCGA-CG-5724 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-CG-5725         TCGA-CG-5726         TCGA-CG-5727 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-CG-5728         TCGA-CG-5730         TCGA-CG-5732 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-CG-5733         TCGA-CG-5734         TCGA-D7-5577 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-D7-5578         TCGA-D7-5579         TCGA-D7-6518 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-D7-6519         TCGA-D7-6520         TCGA-D7-6521 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-D7-6522         TCGA-D7-6524         TCGA-D7-6525 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-D7-6526         TCGA-D7-6527         TCGA-D7-6528 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-D7-6815         TCGA-D7-6817         TCGA-D7-6818 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-D7-6820         TCGA-D7-6822         TCGA-F1-6177 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-F1-6874         TCGA-F1-6875         TCGA-FP-7735 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-FP-7829         TCGA-FP-7998         TCGA-HF-7131 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-HF-7132         TCGA-HF-7133         TCGA-HF-7134 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-HF-7136         TCGA-IN-7806         TCGA-IN-7808 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-IP-7968 
"14Q GAIN WILD-TYPE" 
                    vv
clus                 N0 N1 N2 N3
  14Q GAIN CNV        0  1  0  1
  14Q GAIN WILD-TYPE 44 48 23 14
D25V6, multiclass
[1] "Remove cluster labels:" "14Q GAIN CNV"          
clus
      14Q GAIN CNV 14Q GAIN WILD-TYPE 
                 2                129 
        TCGA-B7-5816         TCGA-B7-5818         TCGA-BR-4183 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-BR-4184         TCGA-BR-4188         TCGA-BR-4191 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-BR-4253         TCGA-BR-4255         TCGA-BR-4256 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-BR-4267         TCGA-BR-4279         TCGA-BR-4280 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-BR-4361         TCGA-BR-4362         TCGA-BR-4367 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-BR-4368         TCGA-BR-6452         TCGA-BR-6453 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-BR-6454         TCGA-BR-6455         TCGA-BR-6456 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-BR-6457         TCGA-BR-6458         TCGA-BR-6563 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-BR-6564         TCGA-BR-6565         TCGA-BR-6566 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-BR-6705         TCGA-BR-6706         TCGA-BR-6707 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-BR-6709         TCGA-BR-6710         TCGA-BR-6801 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-BR-6802         TCGA-BR-6803         TCGA-BR-6852 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-BR-7196         TCGA-BR-7197         TCGA-BR-7703 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-BR-7704         TCGA-BR-7707         TCGA-BR-7715 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-BR-7716         TCGA-BR-7717         TCGA-BR-7722 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-BR-7723         TCGA-BR-7851         TCGA-BR-7901 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-BR-7957         TCGA-CD-5798         TCGA-CD-5799 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-CD-5800         TCGA-CD-5801         TCGA-CD-5802 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-CD-5803         TCGA-CD-5804         TCGA-CG-4300 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-CG-4301         TCGA-CG-4304         TCGA-CG-4305 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-CG-4306         TCGA-CG-4436         TCGA-CG-4437 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-CG-4438         TCGA-CG-4440         TCGA-CG-4441 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-CG-4442         TCGA-CG-4443         TCGA-CG-4444 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-CG-4449         TCGA-CG-4455         TCGA-CG-4462 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-CG-4465         TCGA-CG-4466         TCGA-CG-4469 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-CG-4472         TCGA-CG-4474         TCGA-CG-4475 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-CG-4476         TCGA-CG-4477         TCGA-CG-5716 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-CG-5717         TCGA-CG-5718         TCGA-CG-5719 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-CG-5720         TCGA-CG-5721         TCGA-CG-5722 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-CG-5723         TCGA-CG-5724         TCGA-CG-5725 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-CG-5726         TCGA-CG-5727         TCGA-CG-5728 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-CG-5730         TCGA-CG-5732         TCGA-CG-5733 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-CG-5734         TCGA-D7-5577         TCGA-D7-5578 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-D7-5579         TCGA-D7-6518         TCGA-D7-6519 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-D7-6520         TCGA-D7-6521         TCGA-D7-6522 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-D7-6524         TCGA-D7-6525         TCGA-D7-6526 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-D7-6527         TCGA-D7-6528         TCGA-D7-6815 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-D7-6817         TCGA-D7-6818         TCGA-D7-6820 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-D7-6822         TCGA-F1-6177         TCGA-F1-6874 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-F1-6875         TCGA-FP-7735         TCGA-FP-7829 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-FP-7998         TCGA-HF-7131         TCGA-HF-7132 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-HF-7133         TCGA-HF-7134         TCGA-HF-7136 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-IN-7806         TCGA-IN-7808         TCGA-IP-7968 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
                    vv
clus                  M0  M1  MX
  14Q GAIN CNV         0   2   0
  14Q GAIN WILD-TYPE 118  14   8
D25V7, multiclass
[1] "Remove cluster labels:" "14Q GAIN CNV"          
clus
      14Q GAIN CNV 14Q GAIN WILD-TYPE 
                 2                140 
        TCGA-B7-5816         TCGA-B7-5818         TCGA-BR-4183 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-BR-4184         TCGA-BR-4187         TCGA-BR-4188 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-BR-4191         TCGA-BR-4201         TCGA-BR-4253 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-BR-4255         TCGA-BR-4256         TCGA-BR-4257 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-BR-4267         TCGA-BR-4279         TCGA-BR-4280 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-BR-4292         TCGA-BR-4294         TCGA-BR-4357 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-BR-4361         TCGA-BR-4362         TCGA-BR-4363 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-BR-4366         TCGA-BR-4367         TCGA-BR-4368 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-BR-4369         TCGA-BR-4370         TCGA-BR-4371 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-BR-6452         TCGA-BR-6453         TCGA-BR-6454 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-BR-6455         TCGA-BR-6456         TCGA-BR-6457 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-BR-6458         TCGA-BR-6563         TCGA-BR-6564 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-BR-6565         TCGA-BR-6566         TCGA-BR-6705 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-BR-6706         TCGA-BR-6707         TCGA-BR-6709 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-BR-6710         TCGA-BR-6801         TCGA-BR-6802 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-BR-6803         TCGA-BR-6852         TCGA-BR-7196 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-BR-7197         TCGA-BR-7703         TCGA-BR-7704 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-BR-7707         TCGA-BR-7715         TCGA-BR-7716 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-BR-7717         TCGA-BR-7722         TCGA-BR-7723 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-BR-7851         TCGA-BR-7901         TCGA-BR-7957 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-CD-5798         TCGA-CD-5799         TCGA-CD-5800 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-CD-5801         TCGA-CD-5802         TCGA-CD-5803 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-CD-5804         TCGA-CG-4300         TCGA-CG-4301 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-CG-4304         TCGA-CG-4305         TCGA-CG-4306 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-CG-4436         TCGA-CG-4437         TCGA-CG-4438 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-CG-4440         TCGA-CG-4441         TCGA-CG-4442 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-CG-4443         TCGA-CG-4444         TCGA-CG-4449 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-CG-4455         TCGA-CG-4462         TCGA-CG-4465 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-CG-4466         TCGA-CG-4469         TCGA-CG-4472 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-CG-4474         TCGA-CG-4475         TCGA-CG-4476 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-CG-4477         TCGA-CG-5716         TCGA-CG-5717 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-CG-5718         TCGA-CG-5719         TCGA-CG-5720 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-CG-5721         TCGA-CG-5722         TCGA-CG-5723 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-CG-5724         TCGA-CG-5725         TCGA-CG-5726 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-CG-5727         TCGA-CG-5728         TCGA-CG-5730 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-CG-5732         TCGA-CG-5733         TCGA-CG-5734 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-D7-5577         TCGA-D7-5578         TCGA-D7-5579 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-D7-6518         TCGA-D7-6519         TCGA-D7-6520 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-D7-6521         TCGA-D7-6522         TCGA-D7-6524 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-D7-6525         TCGA-D7-6526         TCGA-D7-6527 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-D7-6528         TCGA-D7-6815         TCGA-D7-6817 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-D7-6818         TCGA-D7-6820         TCGA-D7-6822 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-F1-6177         TCGA-F1-6874         TCGA-F1-6875 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-FP-7735         TCGA-FP-7829         TCGA-FP-7998 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-HF-7131         TCGA-HF-7132         TCGA-HF-7133 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-HF-7134         TCGA-HF-7136         TCGA-IN-7806 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-IN-7808         TCGA-IP-7968 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
                    vv
clus                  I II III IV
  14Q GAIN CNV        0  0   0  2
  14Q GAIN WILD-TYPE 24 37  39 24
D25V8, multiclass
[1] "Remove cluster labels:" "14Q GAIN CNV"          
clus
      14Q GAIN CNV 14Q GAIN WILD-TYPE 
                 2                124 
        TCGA-B7-5816         TCGA-B7-5818         TCGA-BR-4183 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-BR-4184         TCGA-BR-4253         TCGA-BR-4255 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-BR-4267         TCGA-BR-4279         TCGA-BR-4280 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-BR-4361         TCGA-BR-4368         TCGA-BR-6452 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-BR-6453         TCGA-BR-6454         TCGA-BR-6455 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-BR-6456         TCGA-BR-6457         TCGA-BR-6458 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-BR-6563         TCGA-BR-6564         TCGA-BR-6565 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-BR-6566         TCGA-BR-6705         TCGA-BR-6706 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-BR-6707         TCGA-BR-6709         TCGA-BR-6710 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-BR-6801         TCGA-BR-6802         TCGA-BR-6803 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-BR-6852         TCGA-BR-7196         TCGA-BR-7197 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-BR-7703         TCGA-BR-7704         TCGA-BR-7707 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-BR-7715         TCGA-BR-7716         TCGA-BR-7717 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-BR-7722         TCGA-BR-7723         TCGA-BR-7851 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-BR-7901         TCGA-BR-7957         TCGA-CD-5798 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-CD-5799         TCGA-CD-5800         TCGA-CD-5801 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-CD-5802         TCGA-CD-5803         TCGA-CD-5804 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-CG-4300         TCGA-CG-4301         TCGA-CG-4304 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-CG-4305         TCGA-CG-4306         TCGA-CG-4436 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-CG-4437         TCGA-CG-4438         TCGA-CG-4440 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-CG-4441         TCGA-CG-4442         TCGA-CG-4443 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-CG-4444         TCGA-CG-4449         TCGA-CG-4455 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-CG-4462         TCGA-CG-4465         TCGA-CG-4466 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-CG-4469         TCGA-CG-4472         TCGA-CG-4474 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-CG-4475         TCGA-CG-4476         TCGA-CG-4477 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-CG-5716         TCGA-CG-5717         TCGA-CG-5718 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-CG-5719         TCGA-CG-5720         TCGA-CG-5721 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-CG-5722         TCGA-CG-5723         TCGA-CG-5724 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-CG-5725         TCGA-CG-5726         TCGA-CG-5727 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-CG-5728         TCGA-CG-5730         TCGA-CG-5732 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-CG-5733         TCGA-CG-5734         TCGA-D7-5577 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-D7-5578         TCGA-D7-5579         TCGA-D7-6518 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-D7-6519         TCGA-D7-6520         TCGA-D7-6521 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-D7-6522         TCGA-D7-6524         TCGA-D7-6525 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-D7-6526         TCGA-D7-6527         TCGA-D7-6528 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-D7-6815         TCGA-D7-6817         TCGA-D7-6818 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-D7-6820         TCGA-D7-6822         TCGA-F1-6177 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-F1-6874         TCGA-F1-6875         TCGA-FP-7735 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-FP-7829         TCGA-FP-7998         TCGA-HF-7131 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-HF-7132         TCGA-HF-7133         TCGA-HF-7134 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-HF-7136         TCGA-IN-7806         TCGA-IN-7808 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-IP-7968 
"14Q GAIN WILD-TYPE" 
D25V9, binary
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  14Q GAIN CNV          0    3
  14Q GAIN WILD-TYPE    5  172
     clus
vv    14Q GAIN CNV 14Q GAIN WILD-TYPE
  NO             0                  5
  YES            3                172
                    vv
clus                  R0  R1  R2  RX
  14Q GAIN CNV         1   0   2   0
  14Q GAIN WILD-TYPE 124   7  10  25
D25V10, multiclass
    clus
vv   14Q GAIN CNV 14Q GAIN WILD-TYPE
  R0            1                124
  R1            0                  7
  R2            2                 10
  RX            0                 25
D25V11, continuous
[1] "Remove cluster labels:" "14Q GAIN CNV"          
clus
      14Q GAIN CNV 14Q GAIN WILD-TYPE 
                 2                134 
        TCGA-B7-5816         TCGA-BR-4183         TCGA-BR-4184 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-BR-4188         TCGA-BR-4191         TCGA-BR-4253 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-BR-4255         TCGA-BR-4256         TCGA-BR-4267 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-BR-4279         TCGA-BR-4280         TCGA-BR-4361 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-BR-4362         TCGA-BR-4367         TCGA-BR-4368 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-BR-6452         TCGA-BR-6453         TCGA-BR-6454 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-BR-6455         TCGA-BR-6456         TCGA-BR-6457 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-BR-6458         TCGA-BR-6563         TCGA-BR-6564 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-BR-6565         TCGA-BR-6566         TCGA-BR-6705 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-BR-6706         TCGA-BR-6707         TCGA-BR-6709 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-BR-6710         TCGA-BR-6801         TCGA-BR-6802 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-BR-6803         TCGA-BR-6852         TCGA-BR-7196 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-BR-7197         TCGA-BR-7703         TCGA-BR-7704 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-BR-7707         TCGA-BR-7715         TCGA-BR-7716 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-BR-7717         TCGA-BR-7722         TCGA-BR-7723 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-BR-7851         TCGA-BR-7901         TCGA-BR-7957 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-BR-7958         TCGA-BR-7959         TCGA-BR-8059 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-BR-8060         TCGA-BR-8077         TCGA-BR-8078 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-BR-8080         TCGA-BR-8081         TCGA-BR-8284 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-BR-8285         TCGA-BR-8286         TCGA-BR-8289 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-BR-8291         TCGA-BR-8296         TCGA-BR-8297 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-BR-8592         TCGA-BR-A4IU         TCGA-BR-A4IV 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-BR-A4IY         TCGA-BR-A4IZ         TCGA-BR-A4J1 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-BR-A4J2         TCGA-BR-A4J4         TCGA-BR-A4J5 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-BR-A4J6         TCGA-BR-A4J8         TCGA-BR-A4J9 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-BR-A4PF         TCGA-BR-A4QI         TCGA-BR-A4QL 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-CD-5804         TCGA-CG-5717         TCGA-CG-5718 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-CG-5719         TCGA-CG-5720         TCGA-CG-5721 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-CG-5722         TCGA-CG-5723         TCGA-CG-5724 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-CG-5725         TCGA-CG-5726         TCGA-CG-5727 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-CG-5728         TCGA-CG-5730         TCGA-CG-5732 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-CG-5733         TCGA-CG-5734         TCGA-D7-5577 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-D7-5578         TCGA-D7-5579         TCGA-D7-6518 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-D7-6519         TCGA-D7-6520         TCGA-D7-6521 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-D7-6522         TCGA-D7-6524         TCGA-D7-6525 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-D7-6526         TCGA-D7-6527         TCGA-D7-6528 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-D7-6815         TCGA-D7-6817         TCGA-D7-6818 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-D7-6820         TCGA-D7-6822         TCGA-EQ-8122 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-F1-6177         TCGA-F1-6874         TCGA-F1-6875 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-FP-7735         TCGA-FP-7829         TCGA-FP-7916 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-FP-7998         TCGA-FP-8099         TCGA-FP-8209 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-FP-8210         TCGA-FP-8631         TCGA-HF-7131 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-HF-7132         TCGA-HF-7133         TCGA-HF-7134 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-HF-7136         TCGA-HJ-7597         TCGA-IN-7806 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-IN-7808         TCGA-IP-7968 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 

Clustering(26) Variable = 15q gain
D26V1, survival
                    sevent
clus2                  0   1
  15Q GAIN CNV         7   1
  15Q GAIN WILD-TYPE 117  18
      15Q GAIN CNV 15Q GAIN WILD-TYPE 
                 8                135 
      15Q GAIN CNV 15Q GAIN WILD-TYPE 
                 1                 18 
$`15Q GAIN CNV`
TCGA-BR-7197 TCGA-BR-A4J4 TCGA-BR-A4PF TCGA-CG-5727 TCGA-D7-6520 TCGA-F1-6875 
        1.48         0.53         0.72        31.04         9.63        72.23 
TCGA-FP-8099 TCGA-IN-7808 
        1.02         3.55 

$`15Q GAIN WILD-TYPE`
TCGA-B7-5816 TCGA-B7-5818 TCGA-BR-6452 TCGA-BR-6455 TCGA-BR-6457 TCGA-BR-6458 
        5.62         0.10         0.95         1.41         1.35         1.35 
TCGA-BR-6563 TCGA-BR-6564 TCGA-BR-6565 TCGA-BR-6566 TCGA-BR-6705 TCGA-BR-6706 
        0.85         0.82         0.62         0.62         1.71         2.17 
TCGA-BR-6707 TCGA-BR-6709 TCGA-BR-6710 TCGA-BR-6801 TCGA-BR-6802 TCGA-BR-6803 
        0.99         1.22         0.66         1.12         0.76         0.66 
TCGA-BR-6852 TCGA-BR-7196 TCGA-BR-7703 TCGA-BR-7704 TCGA-BR-7707 TCGA-BR-7715 
        0.26         1.22         0.46         1.25         0.13         1.05 
TCGA-BR-7716 TCGA-BR-7717 TCGA-BR-7722 TCGA-BR-7723 TCGA-BR-7851 TCGA-BR-7901 
        0.82         0.69         0.16         4.54         0.99         0.95 
TCGA-BR-7957 TCGA-BR-7958 TCGA-BR-7959 TCGA-BR-8059 TCGA-BR-8060 TCGA-BR-8077 
        0.69         0.16         1.08         0.82         1.32         0.69 
TCGA-BR-8078 TCGA-BR-8080 TCGA-BR-8081 TCGA-BR-8284 TCGA-BR-8285 TCGA-BR-8286 
        0.95         0.49         0.46         0.72         0.26         0.43 
TCGA-BR-8289 TCGA-BR-8291 TCGA-BR-8295 TCGA-BR-8296 TCGA-BR-8297 TCGA-BR-8592 
        0.26         1.18         1.55         1.48         0.76         0.20 
TCGA-BR-A4IU TCGA-BR-A4IV TCGA-BR-A4IY TCGA-BR-A4IZ TCGA-BR-A4J1 TCGA-BR-A4J2 
        0.59         0.92         0.39         0.79         0.72         0.79 
TCGA-BR-A4J5 TCGA-BR-A4J6 TCGA-BR-A4J8 TCGA-BR-A4J9 TCGA-BR-A4QI TCGA-BR-A4QL 
        0.43         0.13         0.23         0.10         0.49         2.24 
TCGA-CD-5798 TCGA-CD-5799 TCGA-CD-5800 TCGA-CD-5801 TCGA-CD-5802 TCGA-CD-5803 
        0.82         0.69         0.36         0.49         0.30         0.07 
TCGA-CG-4300 TCGA-CG-4301 TCGA-CG-4304 TCGA-CG-4305 TCGA-CG-4306 TCGA-CG-4436 
       20.02         3.02        27.02        15.95         1.02        52.96 
TCGA-CG-4437 TCGA-CG-4438 TCGA-CG-4440 TCGA-CG-4441 TCGA-CG-4443 TCGA-CG-4444 
        8.05        54.05         4.01        14.01        29.98        47.05 
TCGA-CG-4449 TCGA-CG-4455 TCGA-CG-4460 TCGA-CG-4462 TCGA-CG-4465 TCGA-CG-4466 
       19.07        12.03        21.99         1.02         8.98        18.94 
TCGA-CG-4469 TCGA-CG-4472 TCGA-CG-4474 TCGA-CG-4477 TCGA-CG-5716 TCGA-CG-5717 
        7.07        12.00         1.02         1.02         1.02         6.94 
TCGA-CG-5718 TCGA-CG-5719 TCGA-CG-5720 TCGA-CG-5721 TCGA-CG-5722 TCGA-CG-5723 
        1.02         1.02         0.99         5.98         0.95        70.06 
TCGA-CG-5724 TCGA-CG-5725 TCGA-CG-5726 TCGA-CG-5728 TCGA-CG-5730 TCGA-CG-5732 
       12.03        15.02        28.96        65.10         4.01        55.04 
TCGA-CG-5733 TCGA-CG-5734 TCGA-D7-5577 TCGA-D7-5578 TCGA-D7-5579 TCGA-D7-6518 
       21.07         7.99         8.65         3.58         4.54         9.80 
TCGA-D7-6519 TCGA-D7-6521 TCGA-D7-6522 TCGA-D7-6524 TCGA-D7-6525 TCGA-D7-6526 
       15.65         8.19         6.90         0.69         5.95         6.61 
TCGA-D7-6527 TCGA-D7-6528 TCGA-D7-6815 TCGA-D7-6817 TCGA-D7-6818 TCGA-D7-6820 
        4.14         1.68         3.65         4.70         4.04         2.93 
TCGA-D7-6822 TCGA-EQ-5647 TCGA-EQ-8122 TCGA-F1-6177 TCGA-F1-6874 TCGA-FP-7735 
        4.27         0.62         7.79         6.54         2.01         0.39 
TCGA-FP-7829 TCGA-FP-7916 TCGA-FP-7998 TCGA-FP-8209 TCGA-FP-8210 TCGA-FP-8631 
        0.20         3.02         3.58        59.05         5.03         0.56 
TCGA-HJ-7597 TCGA-IN-7806 TCGA-IP-7968 
       26.43         6.87         2.53 

      15Q GAIN CNV 15Q GAIN WILD-TYPE 
              0.53               0.07 
      15Q GAIN CNV 15Q GAIN WILD-TYPE 
             72.23              70.06 
      15Q GAIN CNV 15Q GAIN WILD-TYPE 
             2.515              1.220 
[1] "0.5 - 72.2 (2.5)" "0.1 - 70.1 (1.2)"
        TCGA-B7-5816         TCGA-B7-5818         TCGA-BR-6452 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-BR-6455         TCGA-BR-6457         TCGA-BR-6458 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-BR-6563         TCGA-BR-6564         TCGA-BR-6565 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-BR-6566         TCGA-BR-6705         TCGA-BR-6706 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-BR-6707         TCGA-BR-6709         TCGA-BR-6710 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-BR-6801         TCGA-BR-6802         TCGA-BR-6803 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-BR-6852         TCGA-BR-7196         TCGA-BR-7197 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE"       "15Q GAIN CNV" 
        TCGA-BR-7703         TCGA-BR-7704         TCGA-BR-7707 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-BR-7715         TCGA-BR-7716         TCGA-BR-7717 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-BR-7722         TCGA-BR-7723         TCGA-BR-7851 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-BR-7901         TCGA-BR-7957         TCGA-BR-7958 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-BR-7959         TCGA-BR-8059         TCGA-BR-8060 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-BR-8077         TCGA-BR-8078         TCGA-BR-8080 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-BR-8081         TCGA-BR-8284         TCGA-BR-8285 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-BR-8286         TCGA-BR-8289         TCGA-BR-8291 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-BR-8295         TCGA-BR-8296         TCGA-BR-8297 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-BR-8592         TCGA-BR-A4IU         TCGA-BR-A4IV 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-BR-A4IY         TCGA-BR-A4IZ         TCGA-BR-A4J1 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-BR-A4J2         TCGA-BR-A4J4         TCGA-BR-A4J5 
"15Q GAIN WILD-TYPE"       "15Q GAIN CNV" "15Q GAIN WILD-TYPE" 
        TCGA-BR-A4J6         TCGA-BR-A4J8         TCGA-BR-A4J9 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-BR-A4PF         TCGA-BR-A4QI         TCGA-BR-A4QL 
      "15Q GAIN CNV" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-CD-5798         TCGA-CD-5799         TCGA-CD-5800 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-CD-5801         TCGA-CD-5802         TCGA-CD-5803 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-CG-4300         TCGA-CG-4301         TCGA-CG-4304 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-CG-4305         TCGA-CG-4306         TCGA-CG-4436 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-CG-4437         TCGA-CG-4438         TCGA-CG-4440 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-CG-4441         TCGA-CG-4443         TCGA-CG-4444 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-CG-4449         TCGA-CG-4455         TCGA-CG-4460 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-CG-4462         TCGA-CG-4465         TCGA-CG-4466 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-CG-4469         TCGA-CG-4472         TCGA-CG-4474 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-CG-4477         TCGA-CG-5716         TCGA-CG-5717 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-CG-5718         TCGA-CG-5719         TCGA-CG-5720 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-CG-5721         TCGA-CG-5722         TCGA-CG-5723 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-CG-5724         TCGA-CG-5725         TCGA-CG-5726 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-CG-5727         TCGA-CG-5728         TCGA-CG-5730 
      "15Q GAIN CNV" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-CG-5732         TCGA-CG-5733         TCGA-CG-5734 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-D7-5577         TCGA-D7-5578         TCGA-D7-5579 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-D7-6518         TCGA-D7-6519         TCGA-D7-6520 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE"       "15Q GAIN CNV" 
        TCGA-D7-6521         TCGA-D7-6522         TCGA-D7-6524 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-D7-6525         TCGA-D7-6526         TCGA-D7-6527 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-D7-6528         TCGA-D7-6815         TCGA-D7-6817 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-D7-6818         TCGA-D7-6820         TCGA-D7-6822 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-EQ-5647         TCGA-EQ-8122         TCGA-F1-6177 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-F1-6874         TCGA-F1-6875         TCGA-FP-7735 
"15Q GAIN WILD-TYPE"       "15Q GAIN CNV" "15Q GAIN WILD-TYPE" 
        TCGA-FP-7829         TCGA-FP-7916         TCGA-FP-7998 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-FP-8099         TCGA-FP-8209         TCGA-FP-8210 
      "15Q GAIN CNV" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-FP-8631         TCGA-HJ-7597         TCGA-IN-7806 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-IN-7808         TCGA-IP-7968 
      "15Q GAIN CNV" "15Q GAIN WILD-TYPE" 
        TCGA-B7-5816         TCGA-B7-5818         TCGA-BR-6452 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-BR-6455         TCGA-BR-6457         TCGA-BR-6458 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-BR-6563         TCGA-BR-6564         TCGA-BR-6565 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-BR-6566         TCGA-BR-6705         TCGA-BR-6706 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-BR-6707         TCGA-BR-6709         TCGA-BR-6710 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-BR-6801         TCGA-BR-6802         TCGA-BR-6803 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-BR-6852         TCGA-BR-7196         TCGA-BR-7197 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE"       "15Q GAIN CNV" 
        TCGA-BR-7703         TCGA-BR-7704         TCGA-BR-7707 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-BR-7715         TCGA-BR-7716         TCGA-BR-7717 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-BR-7722         TCGA-BR-7723         TCGA-BR-7851 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-BR-7901         TCGA-BR-7957         TCGA-BR-7958 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-BR-7959         TCGA-BR-8059         TCGA-BR-8060 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-BR-8077         TCGA-BR-8078         TCGA-BR-8080 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-BR-8081         TCGA-BR-8284         TCGA-BR-8285 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-BR-8286         TCGA-BR-8289         TCGA-BR-8291 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-BR-8295         TCGA-BR-8296         TCGA-BR-8297 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-BR-8592         TCGA-BR-A4IU         TCGA-BR-A4IV 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-BR-A4IY         TCGA-BR-A4IZ         TCGA-BR-A4J1 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-BR-A4J2         TCGA-BR-A4J4         TCGA-BR-A4J5 
"15Q GAIN WILD-TYPE"       "15Q GAIN CNV" "15Q GAIN WILD-TYPE" 
        TCGA-BR-A4J6         TCGA-BR-A4J8         TCGA-BR-A4J9 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-BR-A4PF         TCGA-BR-A4QI         TCGA-BR-A4QL 
      "15Q GAIN CNV" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-CD-5798         TCGA-CD-5799         TCGA-CD-5800 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-CD-5801         TCGA-CD-5802         TCGA-CD-5803 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-CG-4300         TCGA-CG-4301         TCGA-CG-4304 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-CG-4305         TCGA-CG-4306         TCGA-CG-4436 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-CG-4437         TCGA-CG-4438         TCGA-CG-4440 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-CG-4441         TCGA-CG-4443         TCGA-CG-4444 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-CG-4449         TCGA-CG-4455         TCGA-CG-4460 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-CG-4462         TCGA-CG-4465         TCGA-CG-4466 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-CG-4469         TCGA-CG-4472         TCGA-CG-4474 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-CG-4477         TCGA-CG-5716         TCGA-CG-5717 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-CG-5718         TCGA-CG-5719         TCGA-CG-5720 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-CG-5721         TCGA-CG-5722         TCGA-CG-5723 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-CG-5724         TCGA-CG-5725         TCGA-CG-5726 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-CG-5727         TCGA-CG-5728         TCGA-CG-5730 
      "15Q GAIN CNV" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-CG-5732         TCGA-CG-5733         TCGA-CG-5734 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-D7-5577         TCGA-D7-5578         TCGA-D7-5579 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-D7-6518         TCGA-D7-6519         TCGA-D7-6520 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE"       "15Q GAIN CNV" 
        TCGA-D7-6521         TCGA-D7-6522         TCGA-D7-6524 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-D7-6525         TCGA-D7-6526         TCGA-D7-6527 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-D7-6528         TCGA-D7-6815         TCGA-D7-6817 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-D7-6818         TCGA-D7-6820         TCGA-D7-6822 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-EQ-5647         TCGA-EQ-8122         TCGA-F1-6177 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-F1-6874         TCGA-F1-6875         TCGA-FP-7735 
"15Q GAIN WILD-TYPE"       "15Q GAIN CNV" "15Q GAIN WILD-TYPE" 
        TCGA-FP-7829         TCGA-FP-7916         TCGA-FP-7998 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-FP-8099         TCGA-FP-8209         TCGA-FP-8210 
      "15Q GAIN CNV" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-FP-8631         TCGA-HJ-7597         TCGA-IN-7806 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-IN-7808         TCGA-IP-7968 
      "15Q GAIN CNV" "15Q GAIN WILD-TYPE" 
        TCGA-B7-5816         TCGA-B7-5818         TCGA-BR-6452 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-BR-6455         TCGA-BR-6457         TCGA-BR-6458 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-BR-6563         TCGA-BR-6564         TCGA-BR-6565 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-BR-6566         TCGA-BR-6705         TCGA-BR-6706 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-BR-6707         TCGA-BR-6709         TCGA-BR-6710 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-BR-6801         TCGA-BR-6802         TCGA-BR-6803 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-BR-6852         TCGA-BR-7196         TCGA-BR-7197 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE"       "15Q GAIN CNV" 
        TCGA-BR-7703         TCGA-BR-7704         TCGA-BR-7707 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-BR-7715         TCGA-BR-7716         TCGA-BR-7717 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-BR-7722         TCGA-BR-7723         TCGA-BR-7851 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-BR-7901         TCGA-BR-7957         TCGA-BR-7958 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-BR-7959         TCGA-BR-8059         TCGA-BR-8060 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-BR-8077         TCGA-BR-8078         TCGA-BR-8080 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-BR-8081         TCGA-BR-8284         TCGA-BR-8285 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-BR-8286         TCGA-BR-8289         TCGA-BR-8291 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-BR-8295         TCGA-BR-8296         TCGA-BR-8297 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-BR-8592         TCGA-BR-A4IU         TCGA-BR-A4IV 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-BR-A4IY         TCGA-BR-A4IZ         TCGA-BR-A4J1 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-BR-A4J2         TCGA-BR-A4J4         TCGA-BR-A4J5 
"15Q GAIN WILD-TYPE"       "15Q GAIN CNV" "15Q GAIN WILD-TYPE" 
        TCGA-BR-A4J6         TCGA-BR-A4J8         TCGA-BR-A4J9 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-BR-A4PF         TCGA-BR-A4QI         TCGA-BR-A4QL 
      "15Q GAIN CNV" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-CD-5798         TCGA-CD-5799         TCGA-CD-5800 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-CD-5801         TCGA-CD-5802         TCGA-CD-5803 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-CG-4300         TCGA-CG-4301         TCGA-CG-4304 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-CG-4305         TCGA-CG-4306         TCGA-CG-4436 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-CG-4437         TCGA-CG-4438         TCGA-CG-4440 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-CG-4441         TCGA-CG-4443         TCGA-CG-4444 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-CG-4449         TCGA-CG-4455         TCGA-CG-4460 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-CG-4462         TCGA-CG-4465         TCGA-CG-4466 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-CG-4469         TCGA-CG-4472         TCGA-CG-4474 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-CG-4477         TCGA-CG-5716         TCGA-CG-5717 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-CG-5718         TCGA-CG-5719         TCGA-CG-5720 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-CG-5721         TCGA-CG-5722         TCGA-CG-5723 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-CG-5724         TCGA-CG-5725         TCGA-CG-5726 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-CG-5727         TCGA-CG-5728         TCGA-CG-5730 
      "15Q GAIN CNV" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-CG-5732         TCGA-CG-5733         TCGA-CG-5734 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-D7-5577         TCGA-D7-5578         TCGA-D7-5579 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-D7-6518         TCGA-D7-6519         TCGA-D7-6520 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE"       "15Q GAIN CNV" 
        TCGA-D7-6521         TCGA-D7-6522         TCGA-D7-6524 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-D7-6525         TCGA-D7-6526         TCGA-D7-6527 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-D7-6528         TCGA-D7-6815         TCGA-D7-6817 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-D7-6818         TCGA-D7-6820         TCGA-D7-6822 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-EQ-5647         TCGA-EQ-8122         TCGA-F1-6177 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-F1-6874         TCGA-F1-6875         TCGA-FP-7735 
"15Q GAIN WILD-TYPE"       "15Q GAIN CNV" "15Q GAIN WILD-TYPE" 
        TCGA-FP-7829         TCGA-FP-7916         TCGA-FP-7998 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-FP-8099         TCGA-FP-8209         TCGA-FP-8210 
      "15Q GAIN CNV" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-FP-8631         TCGA-HJ-7597         TCGA-IN-7806 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-IN-7808         TCGA-IP-7968 
      "15Q GAIN CNV" "15Q GAIN WILD-TYPE" 
[1] "hr="     "8.2e+07"
D26V2, continuous
D26V3, binary
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  15Q GAIN CNV          0    8
  15Q GAIN WILD-TYPE   72  100
        clus
vv       15Q GAIN CNV 15Q GAIN WILD-TYPE
  FEMALE            0                 72
  MALE              8                100
                    vv
clus                 STOMACH  ADENOCARCINOMA  DIFFUSE TYPE
  15Q GAIN CNV                                           0
  15Q GAIN WILD-TYPE                                    10
                    vv
clus                 STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  15Q GAIN CNV                                                            3
  15Q GAIN WILD-TYPE                                                     13
                    vv
clus                 STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  15Q GAIN CNV                                                                       0
  15Q GAIN WILD-TYPE                                                                 8
                    vv
clus                 STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE
  15Q GAIN CNV                                                              0
  15Q GAIN WILD-TYPE                                                        3
                    vv
clus                 STOMACH ADENOCARCINOMA  SIGNET RING TYPE
  15Q GAIN CNV                                              0
  15Q GAIN WILD-TYPE                                        1
                    vv
clus                 STOMACH ADENOCARCINOMA - DIFFUSE TYPE
  15Q GAIN CNV                                           1
  15Q GAIN WILD-TYPE                                    15
                    vv
clus                 STOMACH ADENOCARCINOMA - NOT OTHERWISE SPECIFIED (NOS)
  15Q GAIN CNV                                                            2
  15Q GAIN WILD-TYPE                                                     71
                    vv
clus                 STOMACH INTESTINAL ADENOCARCINOMA - MUCINOUS TYPE
  15Q GAIN CNV                                                       0
  15Q GAIN WILD-TYPE                                                 7
                    vv
clus                 STOMACH INTESTINAL ADENOCARCINOMA - PAPILLARY TYPE
  15Q GAIN CNV                                                        0
  15Q GAIN WILD-TYPE                                                  3
                    vv
clus                 STOMACH INTESTINAL ADENOCARCINOMA - TUBULAR TYPE
  15Q GAIN CNV                                                      1
  15Q GAIN WILD-TYPE                                                9
                    vv
clus                 STOMACH INTESTINAL ADENOCARCINOMA - TYPE NOT OTHERWISE SPECIFIED (NOS)
  15Q GAIN CNV                                                                            1
  15Q GAIN WILD-TYPE                                                                     27
D26V4, multiclass
                    vv
clus                 T1 T2 T3 T4
  15Q GAIN CNV        0  2  3  0
  15Q GAIN WILD-TYPE  6 50 53 18
D26V5, multiclass
    clus
vv   15Q GAIN CNV 15Q GAIN WILD-TYPE
  T1            0                  6
  T2            2                 50
  T3            3                 53
  T4            0                 18
                    vv
clus                 N0 N1 N2 N3
  15Q GAIN CNV        3  0  1  1
  15Q GAIN WILD-TYPE 41 49 22 14
D26V6, multiclass
    clus
vv   15Q GAIN CNV 15Q GAIN WILD-TYPE
  N0            3                 41
  N1            0                 49
  N2            1                 22
  N3            1                 14
                    vv
clus                  M0  M1  MX
  15Q GAIN CNV         4   1   0
  15Q GAIN WILD-TYPE 114  15   8
D26V7, multiclass
    clus
vv   15Q GAIN CNV 15Q GAIN WILD-TYPE
  M0            4                114
  M1            1                 15
  MX            0                  8
                    vv
clus                  I II III IV
  15Q GAIN CNV        1  2   2  0
  15Q GAIN WILD-TYPE 23 35  37 26
D26V8, multiclass
     clus
vv    15Q GAIN CNV 15Q GAIN WILD-TYPE
  I              1                 23
  II             2                 35
  III            2                 37
  IV             0                 26
D26V9, binary
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  15Q GAIN CNV          0    8
  15Q GAIN WILD-TYPE    5  167
     clus
vv    15Q GAIN CNV 15Q GAIN WILD-TYPE
  NO             0                  5
  YES            8                167
                    vv
clus                  R0  R1  R2  RX
  15Q GAIN CNV         7   0   0   0
  15Q GAIN WILD-TYPE 118   7  12  25
D26V10, multiclass
    clus
vv   15Q GAIN CNV 15Q GAIN WILD-TYPE
  R0            7                118
  R1            0                  7
  R2            0                 12
  RX            0                 25
D26V11, continuous

Clustering(27) Variable = 16p gain
D27V1, survival
                    sevent
clus2                  0   1
  16P GAIN CNV        10   1
  16P GAIN WILD-TYPE 114  18
      16P GAIN CNV 16P GAIN WILD-TYPE 
                11                132 
      16P GAIN CNV 16P GAIN WILD-TYPE 
                 1                 18 
$`16P GAIN CNV`
TCGA-CG-4438 TCGA-CG-4460 TCGA-CG-4472 TCGA-CG-5719 TCGA-D7-6521 TCGA-D7-6526 
       54.05        21.99        12.00         1.02         8.19         6.61 
TCGA-D7-6817 TCGA-D7-6818 TCGA-FP-7735 TCGA-FP-8099 TCGA-IP-7968 
        4.70         4.04         0.39         1.02         2.53 

$`16P GAIN WILD-TYPE`
TCGA-B7-5816 TCGA-B7-5818 TCGA-BR-6452 TCGA-BR-6455 TCGA-BR-6457 TCGA-BR-6458 
        5.62         0.10         0.95         1.41         1.35         1.35 
TCGA-BR-6563 TCGA-BR-6564 TCGA-BR-6565 TCGA-BR-6566 TCGA-BR-6705 TCGA-BR-6706 
        0.85         0.82         0.62         0.62         1.71         2.17 
TCGA-BR-6707 TCGA-BR-6709 TCGA-BR-6710 TCGA-BR-6801 TCGA-BR-6802 TCGA-BR-6803 
        0.99         1.22         0.66         1.12         0.76         0.66 
TCGA-BR-6852 TCGA-BR-7196 TCGA-BR-7197 TCGA-BR-7703 TCGA-BR-7704 TCGA-BR-7707 
        0.26         1.22         1.48         0.46         1.25         0.13 
TCGA-BR-7715 TCGA-BR-7716 TCGA-BR-7717 TCGA-BR-7722 TCGA-BR-7723 TCGA-BR-7851 
        1.05         0.82         0.69         0.16         4.54         0.99 
TCGA-BR-7901 TCGA-BR-7957 TCGA-BR-7958 TCGA-BR-7959 TCGA-BR-8059 TCGA-BR-8060 
        0.95         0.69         0.16         1.08         0.82         1.32 
TCGA-BR-8077 TCGA-BR-8078 TCGA-BR-8080 TCGA-BR-8081 TCGA-BR-8284 TCGA-BR-8285 
        0.69         0.95         0.49         0.46         0.72         0.26 
TCGA-BR-8286 TCGA-BR-8289 TCGA-BR-8291 TCGA-BR-8295 TCGA-BR-8296 TCGA-BR-8297 
        0.43         0.26         1.18         1.55         1.48         0.76 
TCGA-BR-8592 TCGA-BR-A4IU TCGA-BR-A4IV TCGA-BR-A4IY TCGA-BR-A4IZ TCGA-BR-A4J1 
        0.20         0.59         0.92         0.39         0.79         0.72 
TCGA-BR-A4J2 TCGA-BR-A4J4 TCGA-BR-A4J5 TCGA-BR-A4J6 TCGA-BR-A4J8 TCGA-BR-A4J9 
        0.79         0.53         0.43         0.13         0.23         0.10 
TCGA-BR-A4PF TCGA-BR-A4QI TCGA-BR-A4QL TCGA-CD-5798 TCGA-CD-5799 TCGA-CD-5800 
        0.72         0.49         2.24         0.82         0.69         0.36 
TCGA-CD-5801 TCGA-CD-5802 TCGA-CD-5803 TCGA-CG-4300 TCGA-CG-4301 TCGA-CG-4304 
        0.49         0.30         0.07        20.02         3.02        27.02 
TCGA-CG-4305 TCGA-CG-4306 TCGA-CG-4436 TCGA-CG-4437 TCGA-CG-4440 TCGA-CG-4441 
       15.95         1.02        52.96         8.05         4.01        14.01 
TCGA-CG-4443 TCGA-CG-4444 TCGA-CG-4449 TCGA-CG-4455 TCGA-CG-4462 TCGA-CG-4465 
       29.98        47.05        19.07        12.03         1.02         8.98 
TCGA-CG-4466 TCGA-CG-4469 TCGA-CG-4474 TCGA-CG-4477 TCGA-CG-5716 TCGA-CG-5717 
       18.94         7.07         1.02         1.02         1.02         6.94 
TCGA-CG-5718 TCGA-CG-5720 TCGA-CG-5721 TCGA-CG-5722 TCGA-CG-5723 TCGA-CG-5724 
        1.02         0.99         5.98         0.95        70.06        12.03 
TCGA-CG-5725 TCGA-CG-5726 TCGA-CG-5727 TCGA-CG-5728 TCGA-CG-5730 TCGA-CG-5732 
       15.02        28.96        31.04        65.10         4.01        55.04 
TCGA-CG-5733 TCGA-CG-5734 TCGA-D7-5577 TCGA-D7-5578 TCGA-D7-5579 TCGA-D7-6518 
       21.07         7.99         8.65         3.58         4.54         9.80 
TCGA-D7-6519 TCGA-D7-6520 TCGA-D7-6522 TCGA-D7-6524 TCGA-D7-6525 TCGA-D7-6527 
       15.65         9.63         6.90         0.69         5.95         4.14 
TCGA-D7-6528 TCGA-D7-6815 TCGA-D7-6820 TCGA-D7-6822 TCGA-EQ-5647 TCGA-EQ-8122 
        1.68         3.65         2.93         4.27         0.62         7.79 
TCGA-F1-6177 TCGA-F1-6874 TCGA-F1-6875 TCGA-FP-7829 TCGA-FP-7916 TCGA-FP-7998 
        6.54         2.01        72.23         0.20         3.02         3.58 
TCGA-FP-8209 TCGA-FP-8210 TCGA-FP-8631 TCGA-HJ-7597 TCGA-IN-7806 TCGA-IN-7808 
       59.05         5.03         0.56        26.43         6.87         3.55 

      16P GAIN CNV 16P GAIN WILD-TYPE 
              0.39               0.07 
      16P GAIN CNV 16P GAIN WILD-TYPE 
             54.05              72.23 
      16P GAIN CNV 16P GAIN WILD-TYPE 
               4.7                1.2 
[1] "0.4 - 54.0 (4.7)" "0.1 - 72.2 (1.2)"
        TCGA-B7-5816         TCGA-B7-5818         TCGA-BR-6452 
"16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" 
        TCGA-BR-6455         TCGA-BR-6457         TCGA-BR-6458 
"16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" 
        TCGA-BR-6563         TCGA-BR-6564         TCGA-BR-6565 
"16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" 
        TCGA-BR-6566         TCGA-BR-6705         TCGA-BR-6706 
"16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" 
        TCGA-BR-6707         TCGA-BR-6709         TCGA-BR-6710 
"16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" 
        TCGA-BR-6801         TCGA-BR-6802         TCGA-BR-6803 
"16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" 
        TCGA-BR-6852         TCGA-BR-7196         TCGA-BR-7197 
"16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" 
        TCGA-BR-7703         TCGA-BR-7704         TCGA-BR-7707 
"16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" 
        TCGA-BR-7715         TCGA-BR-7716         TCGA-BR-7717 
"16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" 
        TCGA-BR-7722         TCGA-BR-7723         TCGA-BR-7851 
"16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" 
        TCGA-BR-7901         TCGA-BR-7957         TCGA-BR-7958 
"16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" 
        TCGA-BR-7959         TCGA-BR-8059         TCGA-BR-8060 
"16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" 
        TCGA-BR-8077         TCGA-BR-8078         TCGA-BR-8080 
"16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" 
        TCGA-BR-8081         TCGA-BR-8284         TCGA-BR-8285 
"16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" 
        TCGA-BR-8286         TCGA-BR-8289         TCGA-BR-8291 
"16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" 
        TCGA-BR-8295         TCGA-BR-8296         TCGA-BR-8297 
"16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" 
        TCGA-BR-8592         TCGA-BR-A4IU         TCGA-BR-A4IV 
"16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" 
        TCGA-BR-A4IY         TCGA-BR-A4IZ         TCGA-BR-A4J1 
"16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" 
        TCGA-BR-A4J2         TCGA-BR-A4J4         TCGA-BR-A4J5 
"16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" 
        TCGA-BR-A4J6         TCGA-BR-A4J8         TCGA-BR-A4J9 
"16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" 
        TCGA-BR-A4PF         TCGA-BR-A4QI         TCGA-BR-A4QL 
"16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" 
        TCGA-CD-5798         TCGA-CD-5799         TCGA-CD-5800 
"16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" 
        TCGA-CD-5801         TCGA-CD-5802         TCGA-CD-5803 
"16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" 
        TCGA-CG-4300         TCGA-CG-4301         TCGA-CG-4304 
"16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" 
        TCGA-CG-4305         TCGA-CG-4306         TCGA-CG-4436 
"16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" 
        TCGA-CG-4437         TCGA-CG-4438         TCGA-CG-4440 
"16P GAIN WILD-TYPE"       "16P GAIN CNV" "16P GAIN WILD-TYPE" 
        TCGA-CG-4441         TCGA-CG-4443         TCGA-CG-4444 
"16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" 
        TCGA-CG-4449         TCGA-CG-4455         TCGA-CG-4460 
"16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE"       "16P GAIN CNV" 
        TCGA-CG-4462         TCGA-CG-4465         TCGA-CG-4466 
"16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" 
        TCGA-CG-4469         TCGA-CG-4472         TCGA-CG-4474 
"16P GAIN WILD-TYPE"       "16P GAIN CNV" "16P GAIN WILD-TYPE" 
        TCGA-CG-4477         TCGA-CG-5716         TCGA-CG-5717 
"16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" 
        TCGA-CG-5718         TCGA-CG-5719         TCGA-CG-5720 
"16P GAIN WILD-TYPE"       "16P GAIN CNV" "16P GAIN WILD-TYPE" 
        TCGA-CG-5721         TCGA-CG-5722         TCGA-CG-5723 
"16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" 
        TCGA-CG-5724         TCGA-CG-5725         TCGA-CG-5726 
"16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" 
        TCGA-CG-5727         TCGA-CG-5728         TCGA-CG-5730 
"16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" 
        TCGA-CG-5732         TCGA-CG-5733         TCGA-CG-5734 
"16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" 
        TCGA-D7-5577         TCGA-D7-5578         TCGA-D7-5579 
"16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" 
        TCGA-D7-6518         TCGA-D7-6519         TCGA-D7-6520 
"16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" 
        TCGA-D7-6521         TCGA-D7-6522         TCGA-D7-6524 
      "16P GAIN CNV" "16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" 
        TCGA-D7-6525         TCGA-D7-6526         TCGA-D7-6527 
"16P GAIN WILD-TYPE"       "16P GAIN CNV" "16P GAIN WILD-TYPE" 
        TCGA-D7-6528         TCGA-D7-6815         TCGA-D7-6817 
"16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE"       "16P GAIN CNV" 
        TCGA-D7-6818         TCGA-D7-6820         TCGA-D7-6822 
      "16P GAIN CNV" "16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" 
        TCGA-EQ-5647         TCGA-EQ-8122         TCGA-F1-6177 
"16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" 
        TCGA-F1-6874         TCGA-F1-6875         TCGA-FP-7735 
"16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE"       "16P GAIN CNV" 
        TCGA-FP-7829         TCGA-FP-7916         TCGA-FP-7998 
"16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" 
        TCGA-FP-8099         TCGA-FP-8209         TCGA-FP-8210 
      "16P GAIN CNV" "16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" 
        TCGA-FP-8631         TCGA-HJ-7597         TCGA-IN-7806 
"16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" 
        TCGA-IN-7808         TCGA-IP-7968 
"16P GAIN WILD-TYPE"       "16P GAIN CNV" 
        TCGA-B7-5816         TCGA-B7-5818         TCGA-BR-6452 
"16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" 
        TCGA-BR-6455         TCGA-BR-6457         TCGA-BR-6458 
"16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" 
        TCGA-BR-6563         TCGA-BR-6564         TCGA-BR-6565 
"16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" 
        TCGA-BR-6566         TCGA-BR-6705         TCGA-BR-6706 
"16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" 
        TCGA-BR-6707         TCGA-BR-6709         TCGA-BR-6710 
"16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" 
        TCGA-BR-6801         TCGA-BR-6802         TCGA-BR-6803 
"16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" 
        TCGA-BR-6852         TCGA-BR-7196         TCGA-BR-7197 
"16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" 
        TCGA-BR-7703         TCGA-BR-7704         TCGA-BR-7707 
"16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" 
        TCGA-BR-7715         TCGA-BR-7716         TCGA-BR-7717 
"16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" 
        TCGA-BR-7722         TCGA-BR-7723         TCGA-BR-7851 
"16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" 
        TCGA-BR-7901         TCGA-BR-7957         TCGA-BR-7958 
"16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" 
        TCGA-BR-7959         TCGA-BR-8059         TCGA-BR-8060 
"16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" 
        TCGA-BR-8077         TCGA-BR-8078         TCGA-BR-8080 
"16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" 
        TCGA-BR-8081         TCGA-BR-8284         TCGA-BR-8285 
"16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" 
        TCGA-BR-8286         TCGA-BR-8289         TCGA-BR-8291 
"16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" 
        TCGA-BR-8295         TCGA-BR-8296         TCGA-BR-8297 
"16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" 
        TCGA-BR-8592         TCGA-BR-A4IU         TCGA-BR-A4IV 
"16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" 
        TCGA-BR-A4IY         TCGA-BR-A4IZ         TCGA-BR-A4J1 
"16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" 
        TCGA-BR-A4J2         TCGA-BR-A4J4         TCGA-BR-A4J5 
"16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" 
        TCGA-BR-A4J6         TCGA-BR-A4J8         TCGA-BR-A4J9 
"16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" 
        TCGA-BR-A4PF         TCGA-BR-A4QI         TCGA-BR-A4QL 
"16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" 
        TCGA-CD-5798         TCGA-CD-5799         TCGA-CD-5800 
"16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" 
        TCGA-CD-5801         TCGA-CD-5802         TCGA-CD-5803 
"16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" 
        TCGA-CG-4300         TCGA-CG-4301         TCGA-CG-4304 
"16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" 
        TCGA-CG-4305         TCGA-CG-4306         TCGA-CG-4436 
"16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" 
        TCGA-CG-4437         TCGA-CG-4438         TCGA-CG-4440 
"16P GAIN WILD-TYPE"       "16P GAIN CNV" "16P GAIN WILD-TYPE" 
        TCGA-CG-4441         TCGA-CG-4443         TCGA-CG-4444 
"16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" 
        TCGA-CG-4449         TCGA-CG-4455         TCGA-CG-4460 
"16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE"       "16P GAIN CNV" 
        TCGA-CG-4462         TCGA-CG-4465         TCGA-CG-4466 
"16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" 
        TCGA-CG-4469         TCGA-CG-4472         TCGA-CG-4474 
"16P GAIN WILD-TYPE"       "16P GAIN CNV" "16P GAIN WILD-TYPE" 
        TCGA-CG-4477         TCGA-CG-5716         TCGA-CG-5717 
"16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" 
        TCGA-CG-5718         TCGA-CG-5719         TCGA-CG-5720 
"16P GAIN WILD-TYPE"       "16P GAIN CNV" "16P GAIN WILD-TYPE" 
        TCGA-CG-5721         TCGA-CG-5722         TCGA-CG-5723 
"16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" 
        TCGA-CG-5724         TCGA-CG-5725         TCGA-CG-5726 
"16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" 
        TCGA-CG-5727         TCGA-CG-5728         TCGA-CG-5730 
"16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" 
        TCGA-CG-5732         TCGA-CG-5733         TCGA-CG-5734 
"16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" 
        TCGA-D7-5577         TCGA-D7-5578         TCGA-D7-5579 
"16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" 
        TCGA-D7-6518         TCGA-D7-6519         TCGA-D7-6520 
"16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" 
        TCGA-D7-6521         TCGA-D7-6522         TCGA-D7-6524 
      "16P GAIN CNV" "16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" 
        TCGA-D7-6525         TCGA-D7-6526         TCGA-D7-6527 
"16P GAIN WILD-TYPE"       "16P GAIN CNV" "16P GAIN WILD-TYPE" 
        TCGA-D7-6528         TCGA-D7-6815         TCGA-D7-6817 
"16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE"       "16P GAIN CNV" 
        TCGA-D7-6818         TCGA-D7-6820         TCGA-D7-6822 
      "16P GAIN CNV" "16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" 
        TCGA-EQ-5647         TCGA-EQ-8122         TCGA-F1-6177 
"16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" 
        TCGA-F1-6874         TCGA-F1-6875         TCGA-FP-7735 
"16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE"       "16P GAIN CNV" 
        TCGA-FP-7829         TCGA-FP-7916         TCGA-FP-7998 
"16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" 
        TCGA-FP-8099         TCGA-FP-8209         TCGA-FP-8210 
      "16P GAIN CNV" "16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" 
        TCGA-FP-8631         TCGA-HJ-7597         TCGA-IN-7806 
"16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" 
        TCGA-IN-7808         TCGA-IP-7968 
"16P GAIN WILD-TYPE"       "16P GAIN CNV" 
        TCGA-B7-5816         TCGA-B7-5818         TCGA-BR-6452 
"16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" 
        TCGA-BR-6455         TCGA-BR-6457         TCGA-BR-6458 
"16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" 
        TCGA-BR-6563         TCGA-BR-6564         TCGA-BR-6565 
"16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" 
        TCGA-BR-6566         TCGA-BR-6705         TCGA-BR-6706 
"16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" 
        TCGA-BR-6707         TCGA-BR-6709         TCGA-BR-6710 
"16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" 
        TCGA-BR-6801         TCGA-BR-6802         TCGA-BR-6803 
"16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" 
        TCGA-BR-6852         TCGA-BR-7196         TCGA-BR-7197 
"16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" 
        TCGA-BR-7703         TCGA-BR-7704         TCGA-BR-7707 
"16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" 
        TCGA-BR-7715         TCGA-BR-7716         TCGA-BR-7717 
"16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" 
        TCGA-BR-7722         TCGA-BR-7723         TCGA-BR-7851 
"16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" 
        TCGA-BR-7901         TCGA-BR-7957         TCGA-BR-7958 
"16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" 
        TCGA-BR-7959         TCGA-BR-8059         TCGA-BR-8060 
"16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" 
        TCGA-BR-8077         TCGA-BR-8078         TCGA-BR-8080 
"16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" 
        TCGA-BR-8081         TCGA-BR-8284         TCGA-BR-8285 
"16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" 
        TCGA-BR-8286         TCGA-BR-8289         TCGA-BR-8291 
"16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" 
        TCGA-BR-8295         TCGA-BR-8296         TCGA-BR-8297 
"16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" 
        TCGA-BR-8592         TCGA-BR-A4IU         TCGA-BR-A4IV 
"16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" 
        TCGA-BR-A4IY         TCGA-BR-A4IZ         TCGA-BR-A4J1 
"16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" 
        TCGA-BR-A4J2         TCGA-BR-A4J4         TCGA-BR-A4J5 
"16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" 
        TCGA-BR-A4J6         TCGA-BR-A4J8         TCGA-BR-A4J9 
"16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" 
        TCGA-BR-A4PF         TCGA-BR-A4QI         TCGA-BR-A4QL 
"16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" 
        TCGA-CD-5798         TCGA-CD-5799         TCGA-CD-5800 
"16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" 
        TCGA-CD-5801         TCGA-CD-5802         TCGA-CD-5803 
"16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" 
        TCGA-CG-4300         TCGA-CG-4301         TCGA-CG-4304 
"16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" 
        TCGA-CG-4305         TCGA-CG-4306         TCGA-CG-4436 
"16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" 
        TCGA-CG-4437         TCGA-CG-4438         TCGA-CG-4440 
"16P GAIN WILD-TYPE"       "16P GAIN CNV" "16P GAIN WILD-TYPE" 
        TCGA-CG-4441         TCGA-CG-4443         TCGA-CG-4444 
"16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" 
        TCGA-CG-4449         TCGA-CG-4455         TCGA-CG-4460 
"16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE"       "16P GAIN CNV" 
        TCGA-CG-4462         TCGA-CG-4465         TCGA-CG-4466 
"16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" 
        TCGA-CG-4469         TCGA-CG-4472         TCGA-CG-4474 
"16P GAIN WILD-TYPE"       "16P GAIN CNV" "16P GAIN WILD-TYPE" 
        TCGA-CG-4477         TCGA-CG-5716         TCGA-CG-5717 
"16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" 
        TCGA-CG-5718         TCGA-CG-5719         TCGA-CG-5720 
"16P GAIN WILD-TYPE"       "16P GAIN CNV" "16P GAIN WILD-TYPE" 
        TCGA-CG-5721         TCGA-CG-5722         TCGA-CG-5723 
"16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" 
        TCGA-CG-5724         TCGA-CG-5725         TCGA-CG-5726 
"16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" 
        TCGA-CG-5727         TCGA-CG-5728         TCGA-CG-5730 
"16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" 
        TCGA-CG-5732         TCGA-CG-5733         TCGA-CG-5734 
"16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" 
        TCGA-D7-5577         TCGA-D7-5578         TCGA-D7-5579 
"16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" 
        TCGA-D7-6518         TCGA-D7-6519         TCGA-D7-6520 
"16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" 
        TCGA-D7-6521         TCGA-D7-6522         TCGA-D7-6524 
      "16P GAIN CNV" "16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" 
        TCGA-D7-6525         TCGA-D7-6526         TCGA-D7-6527 
"16P GAIN WILD-TYPE"       "16P GAIN CNV" "16P GAIN WILD-TYPE" 
        TCGA-D7-6528         TCGA-D7-6815         TCGA-D7-6817 
"16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE"       "16P GAIN CNV" 
        TCGA-D7-6818         TCGA-D7-6820         TCGA-D7-6822 
      "16P GAIN CNV" "16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" 
        TCGA-EQ-5647         TCGA-EQ-8122         TCGA-F1-6177 
"16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" 
        TCGA-F1-6874         TCGA-F1-6875         TCGA-FP-7735 
"16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE"       "16P GAIN CNV" 
        TCGA-FP-7829         TCGA-FP-7916         TCGA-FP-7998 
"16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" 
        TCGA-FP-8099         TCGA-FP-8209         TCGA-FP-8210 
      "16P GAIN CNV" "16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" 
        TCGA-FP-8631         TCGA-HJ-7597         TCGA-IN-7806 
"16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" 
        TCGA-IN-7808         TCGA-IP-7968 
"16P GAIN WILD-TYPE"       "16P GAIN CNV" 
[1] "hr=" "1.9"
D27V2, continuous
D27V3, binary
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  16P GAIN CNV          4    9
  16P GAIN WILD-TYPE   68   99
        clus
vv       16P GAIN CNV 16P GAIN WILD-TYPE
  FEMALE            4                 68
  MALE              9                 99
                    vv
clus                 STOMACH  ADENOCARCINOMA  DIFFUSE TYPE
  16P GAIN CNV                                           0
  16P GAIN WILD-TYPE                                    10
                    vv
clus                 STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  16P GAIN CNV                                                            1
  16P GAIN WILD-TYPE                                                     15
                    vv
clus                 STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  16P GAIN CNV                                                                       0
  16P GAIN WILD-TYPE                                                                 8
                    vv
clus                 STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE
  16P GAIN CNV                                                              0
  16P GAIN WILD-TYPE                                                        3
                    vv
clus                 STOMACH ADENOCARCINOMA  SIGNET RING TYPE
  16P GAIN CNV                                              0
  16P GAIN WILD-TYPE                                        1
                    vv
clus                 STOMACH ADENOCARCINOMA - DIFFUSE TYPE
  16P GAIN CNV                                           2
  16P GAIN WILD-TYPE                                    14
                    vv
clus                 STOMACH ADENOCARCINOMA - NOT OTHERWISE SPECIFIED (NOS)
  16P GAIN CNV                                                            4
  16P GAIN WILD-TYPE                                                     69
                    vv
clus                 STOMACH INTESTINAL ADENOCARCINOMA - MUCINOUS TYPE
  16P GAIN CNV                                                       0
  16P GAIN WILD-TYPE                                                 7
                    vv
clus                 STOMACH INTESTINAL ADENOCARCINOMA - PAPILLARY TYPE
  16P GAIN CNV                                                        0
  16P GAIN WILD-TYPE                                                  3
                    vv
clus                 STOMACH INTESTINAL ADENOCARCINOMA - TUBULAR TYPE
  16P GAIN CNV                                                      2
  16P GAIN WILD-TYPE                                                8
                    vv
clus                 STOMACH INTESTINAL ADENOCARCINOMA - TYPE NOT OTHERWISE SPECIFIED (NOS)
  16P GAIN CNV                                                                            3
  16P GAIN WILD-TYPE                                                                     25
D27V4, multiclass
                    vv
clus                 T1 T2 T3 T4
  16P GAIN CNV        0  4  3  5
  16P GAIN WILD-TYPE  6 48 53 13
D27V5, multiclass
    clus
vv   16P GAIN CNV 16P GAIN WILD-TYPE
  T1            0                  6
  T2            4                 48
  T3            3                 53
  T4            5                 13
                    vv
clus                 N0 N1 N2 N3
  16P GAIN CNV        2  3  5  2
  16P GAIN WILD-TYPE 42 46 18 13
D27V6, multiclass
    clus
vv   16P GAIN CNV 16P GAIN WILD-TYPE
  N0            2                 42
  N1            3                 46
  N2            5                 18
  N3            2                 13
                    vv
clus                  M0  M1  MX
  16P GAIN CNV         8   2   2
  16P GAIN WILD-TYPE 110  14   6
D27V7, multiclass
    clus
vv   16P GAIN CNV 16P GAIN WILD-TYPE
  M0            8                110
  M1            2                 14
  MX            2                  6
                    vv
clus                  I II III IV
  16P GAIN CNV        1  0   5  6
  16P GAIN WILD-TYPE 23 37  34 20
D27V8, multiclass
     clus
vv    16P GAIN CNV 16P GAIN WILD-TYPE
  I              1                 23
  II             0                 37
  III            5                 34
  IV             6                 20
D27V9, binary
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  16P GAIN CNV          1   12
  16P GAIN WILD-TYPE    4  163
     clus
vv    16P GAIN CNV 16P GAIN WILD-TYPE
  NO             1                  4
  YES           12                163
                    vv
clus                  R0  R1  R2  RX
  16P GAIN CNV        10   0   1   1
  16P GAIN WILD-TYPE 115   7  11  24
D27V10, multiclass
    clus
vv   16P GAIN CNV 16P GAIN WILD-TYPE
  R0           10                115
  R1            0                  7
  R2            1                 11
  RX            1                 24
D27V11, continuous

Clustering(28) Variable = 16q gain
D28V1, survival
                    sevent
clus2                  0   1
  16Q GAIN CNV         7   1
  16Q GAIN WILD-TYPE 117  18
      16Q GAIN CNV 16Q GAIN WILD-TYPE 
                 8                135 
      16Q GAIN CNV 16Q GAIN WILD-TYPE 
                 1                 18 
$`16Q GAIN CNV`
TCGA-CG-4438 TCGA-CG-4460 TCGA-CG-4472 TCGA-CG-5719 TCGA-D7-6521 TCGA-EQ-8122 
       54.05        21.99        12.00         1.02         8.19         7.79 
TCGA-FP-7735 TCGA-FP-8099 
        0.39         1.02 

$`16Q GAIN WILD-TYPE`
TCGA-B7-5816 TCGA-B7-5818 TCGA-BR-6452 TCGA-BR-6455 TCGA-BR-6457 TCGA-BR-6458 
        5.62         0.10         0.95         1.41         1.35         1.35 
TCGA-BR-6563 TCGA-BR-6564 TCGA-BR-6565 TCGA-BR-6566 TCGA-BR-6705 TCGA-BR-6706 
        0.85         0.82         0.62         0.62         1.71         2.17 
TCGA-BR-6707 TCGA-BR-6709 TCGA-BR-6710 TCGA-BR-6801 TCGA-BR-6802 TCGA-BR-6803 
        0.99         1.22         0.66         1.12         0.76         0.66 
TCGA-BR-6852 TCGA-BR-7196 TCGA-BR-7197 TCGA-BR-7703 TCGA-BR-7704 TCGA-BR-7707 
        0.26         1.22         1.48         0.46         1.25         0.13 
TCGA-BR-7715 TCGA-BR-7716 TCGA-BR-7717 TCGA-BR-7722 TCGA-BR-7723 TCGA-BR-7851 
        1.05         0.82         0.69         0.16         4.54         0.99 
TCGA-BR-7901 TCGA-BR-7957 TCGA-BR-7958 TCGA-BR-7959 TCGA-BR-8059 TCGA-BR-8060 
        0.95         0.69         0.16         1.08         0.82         1.32 
TCGA-BR-8077 TCGA-BR-8078 TCGA-BR-8080 TCGA-BR-8081 TCGA-BR-8284 TCGA-BR-8285 
        0.69         0.95         0.49         0.46         0.72         0.26 
TCGA-BR-8286 TCGA-BR-8289 TCGA-BR-8291 TCGA-BR-8295 TCGA-BR-8296 TCGA-BR-8297 
        0.43         0.26         1.18         1.55         1.48         0.76 
TCGA-BR-8592 TCGA-BR-A4IU TCGA-BR-A4IV TCGA-BR-A4IY TCGA-BR-A4IZ TCGA-BR-A4J1 
        0.20         0.59         0.92         0.39         0.79         0.72 
TCGA-BR-A4J2 TCGA-BR-A4J4 TCGA-BR-A4J5 TCGA-BR-A4J6 TCGA-BR-A4J8 TCGA-BR-A4J9 
        0.79         0.53         0.43         0.13         0.23         0.10 
TCGA-BR-A4PF TCGA-BR-A4QI TCGA-BR-A4QL TCGA-CD-5798 TCGA-CD-5799 TCGA-CD-5800 
        0.72         0.49         2.24         0.82         0.69         0.36 
TCGA-CD-5801 TCGA-CD-5802 TCGA-CD-5803 TCGA-CG-4300 TCGA-CG-4301 TCGA-CG-4304 
        0.49         0.30         0.07        20.02         3.02        27.02 
TCGA-CG-4305 TCGA-CG-4306 TCGA-CG-4436 TCGA-CG-4437 TCGA-CG-4440 TCGA-CG-4441 
       15.95         1.02        52.96         8.05         4.01        14.01 
TCGA-CG-4443 TCGA-CG-4444 TCGA-CG-4449 TCGA-CG-4455 TCGA-CG-4462 TCGA-CG-4465 
       29.98        47.05        19.07        12.03         1.02         8.98 
TCGA-CG-4466 TCGA-CG-4469 TCGA-CG-4474 TCGA-CG-4477 TCGA-CG-5716 TCGA-CG-5717 
       18.94         7.07         1.02         1.02         1.02         6.94 
TCGA-CG-5718 TCGA-CG-5720 TCGA-CG-5721 TCGA-CG-5722 TCGA-CG-5723 TCGA-CG-5724 
        1.02         0.99         5.98         0.95        70.06        12.03 
TCGA-CG-5725 TCGA-CG-5726 TCGA-CG-5727 TCGA-CG-5728 TCGA-CG-5730 TCGA-CG-5732 
       15.02        28.96        31.04        65.10         4.01        55.04 
TCGA-CG-5733 TCGA-CG-5734 TCGA-D7-5577 TCGA-D7-5578 TCGA-D7-5579 TCGA-D7-6518 
       21.07         7.99         8.65         3.58         4.54         9.80 
TCGA-D7-6519 TCGA-D7-6520 TCGA-D7-6522 TCGA-D7-6524 TCGA-D7-6525 TCGA-D7-6526 
       15.65         9.63         6.90         0.69         5.95         6.61 
TCGA-D7-6527 TCGA-D7-6528 TCGA-D7-6815 TCGA-D7-6817 TCGA-D7-6818 TCGA-D7-6820 
        4.14         1.68         3.65         4.70         4.04         2.93 
TCGA-D7-6822 TCGA-EQ-5647 TCGA-F1-6177 TCGA-F1-6874 TCGA-F1-6875 TCGA-FP-7829 
        4.27         0.62         6.54         2.01        72.23         0.20 
TCGA-FP-7916 TCGA-FP-7998 TCGA-FP-8209 TCGA-FP-8210 TCGA-FP-8631 TCGA-HJ-7597 
        3.02         3.58        59.05         5.03         0.56        26.43 
TCGA-IN-7806 TCGA-IN-7808 TCGA-IP-7968 
        6.87         3.55         2.53 

      16Q GAIN CNV 16Q GAIN WILD-TYPE 
              0.39               0.07 
      16Q GAIN CNV 16Q GAIN WILD-TYPE 
             54.05              72.23 
      16Q GAIN CNV 16Q GAIN WILD-TYPE 
              7.99               1.22 
[1] "0.4 - 54.0 (8.0)" "0.1 - 72.2 (1.2)"
        TCGA-B7-5816         TCGA-B7-5818         TCGA-BR-6452 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-BR-6455         TCGA-BR-6457         TCGA-BR-6458 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-BR-6563         TCGA-BR-6564         TCGA-BR-6565 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-BR-6566         TCGA-BR-6705         TCGA-BR-6706 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-BR-6707         TCGA-BR-6709         TCGA-BR-6710 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-BR-6801         TCGA-BR-6802         TCGA-BR-6803 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-BR-6852         TCGA-BR-7196         TCGA-BR-7197 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-BR-7703         TCGA-BR-7704         TCGA-BR-7707 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-BR-7715         TCGA-BR-7716         TCGA-BR-7717 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-BR-7722         TCGA-BR-7723         TCGA-BR-7851 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-BR-7901         TCGA-BR-7957         TCGA-BR-7958 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-BR-7959         TCGA-BR-8059         TCGA-BR-8060 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-BR-8077         TCGA-BR-8078         TCGA-BR-8080 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-BR-8081         TCGA-BR-8284         TCGA-BR-8285 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-BR-8286         TCGA-BR-8289         TCGA-BR-8291 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-BR-8295         TCGA-BR-8296         TCGA-BR-8297 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-BR-8592         TCGA-BR-A4IU         TCGA-BR-A4IV 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-BR-A4IY         TCGA-BR-A4IZ         TCGA-BR-A4J1 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-BR-A4J2         TCGA-BR-A4J4         TCGA-BR-A4J5 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-BR-A4J6         TCGA-BR-A4J8         TCGA-BR-A4J9 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-BR-A4PF         TCGA-BR-A4QI         TCGA-BR-A4QL 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-CD-5798         TCGA-CD-5799         TCGA-CD-5800 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-CD-5801         TCGA-CD-5802         TCGA-CD-5803 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-CG-4300         TCGA-CG-4301         TCGA-CG-4304 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-CG-4305         TCGA-CG-4306         TCGA-CG-4436 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-CG-4437         TCGA-CG-4438         TCGA-CG-4440 
"16Q GAIN WILD-TYPE"       "16Q GAIN CNV" "16Q GAIN WILD-TYPE" 
        TCGA-CG-4441         TCGA-CG-4443         TCGA-CG-4444 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-CG-4449         TCGA-CG-4455         TCGA-CG-4460 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE"       "16Q GAIN CNV" 
        TCGA-CG-4462         TCGA-CG-4465         TCGA-CG-4466 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-CG-4469         TCGA-CG-4472         TCGA-CG-4474 
"16Q GAIN WILD-TYPE"       "16Q GAIN CNV" "16Q GAIN WILD-TYPE" 
        TCGA-CG-4477         TCGA-CG-5716         TCGA-CG-5717 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-CG-5718         TCGA-CG-5719         TCGA-CG-5720 
"16Q GAIN WILD-TYPE"       "16Q GAIN CNV" "16Q GAIN WILD-TYPE" 
        TCGA-CG-5721         TCGA-CG-5722         TCGA-CG-5723 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-CG-5724         TCGA-CG-5725         TCGA-CG-5726 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-CG-5727         TCGA-CG-5728         TCGA-CG-5730 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-CG-5732         TCGA-CG-5733         TCGA-CG-5734 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-D7-5577         TCGA-D7-5578         TCGA-D7-5579 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-D7-6518         TCGA-D7-6519         TCGA-D7-6520 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-D7-6521         TCGA-D7-6522         TCGA-D7-6524 
      "16Q GAIN CNV" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-D7-6525         TCGA-D7-6526         TCGA-D7-6527 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-D7-6528         TCGA-D7-6815         TCGA-D7-6817 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-D7-6818         TCGA-D7-6820         TCGA-D7-6822 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-EQ-5647         TCGA-EQ-8122         TCGA-F1-6177 
"16Q GAIN WILD-TYPE"       "16Q GAIN CNV" "16Q GAIN WILD-TYPE" 
        TCGA-F1-6874         TCGA-F1-6875         TCGA-FP-7735 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE"       "16Q GAIN CNV" 
        TCGA-FP-7829         TCGA-FP-7916         TCGA-FP-7998 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-FP-8099         TCGA-FP-8209         TCGA-FP-8210 
      "16Q GAIN CNV" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-FP-8631         TCGA-HJ-7597         TCGA-IN-7806 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-IN-7808         TCGA-IP-7968 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-B7-5816         TCGA-B7-5818         TCGA-BR-6452 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-BR-6455         TCGA-BR-6457         TCGA-BR-6458 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-BR-6563         TCGA-BR-6564         TCGA-BR-6565 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-BR-6566         TCGA-BR-6705         TCGA-BR-6706 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-BR-6707         TCGA-BR-6709         TCGA-BR-6710 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-BR-6801         TCGA-BR-6802         TCGA-BR-6803 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-BR-6852         TCGA-BR-7196         TCGA-BR-7197 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-BR-7703         TCGA-BR-7704         TCGA-BR-7707 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-BR-7715         TCGA-BR-7716         TCGA-BR-7717 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-BR-7722         TCGA-BR-7723         TCGA-BR-7851 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-BR-7901         TCGA-BR-7957         TCGA-BR-7958 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-BR-7959         TCGA-BR-8059         TCGA-BR-8060 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-BR-8077         TCGA-BR-8078         TCGA-BR-8080 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-BR-8081         TCGA-BR-8284         TCGA-BR-8285 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-BR-8286         TCGA-BR-8289         TCGA-BR-8291 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-BR-8295         TCGA-BR-8296         TCGA-BR-8297 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-BR-8592         TCGA-BR-A4IU         TCGA-BR-A4IV 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-BR-A4IY         TCGA-BR-A4IZ         TCGA-BR-A4J1 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-BR-A4J2         TCGA-BR-A4J4         TCGA-BR-A4J5 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-BR-A4J6         TCGA-BR-A4J8         TCGA-BR-A4J9 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-BR-A4PF         TCGA-BR-A4QI         TCGA-BR-A4QL 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-CD-5798         TCGA-CD-5799         TCGA-CD-5800 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-CD-5801         TCGA-CD-5802         TCGA-CD-5803 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-CG-4300         TCGA-CG-4301         TCGA-CG-4304 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-CG-4305         TCGA-CG-4306         TCGA-CG-4436 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-CG-4437         TCGA-CG-4438         TCGA-CG-4440 
"16Q GAIN WILD-TYPE"       "16Q GAIN CNV" "16Q GAIN WILD-TYPE" 
        TCGA-CG-4441         TCGA-CG-4443         TCGA-CG-4444 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-CG-4449         TCGA-CG-4455         TCGA-CG-4460 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE"       "16Q GAIN CNV" 
        TCGA-CG-4462         TCGA-CG-4465         TCGA-CG-4466 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-CG-4469         TCGA-CG-4472         TCGA-CG-4474 
"16Q GAIN WILD-TYPE"       "16Q GAIN CNV" "16Q GAIN WILD-TYPE" 
        TCGA-CG-4477         TCGA-CG-5716         TCGA-CG-5717 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-CG-5718         TCGA-CG-5719         TCGA-CG-5720 
"16Q GAIN WILD-TYPE"       "16Q GAIN CNV" "16Q GAIN WILD-TYPE" 
        TCGA-CG-5721         TCGA-CG-5722         TCGA-CG-5723 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-CG-5724         TCGA-CG-5725         TCGA-CG-5726 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-CG-5727         TCGA-CG-5728         TCGA-CG-5730 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-CG-5732         TCGA-CG-5733         TCGA-CG-5734 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-D7-5577         TCGA-D7-5578         TCGA-D7-5579 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-D7-6518         TCGA-D7-6519         TCGA-D7-6520 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-D7-6521         TCGA-D7-6522         TCGA-D7-6524 
      "16Q GAIN CNV" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-D7-6525         TCGA-D7-6526         TCGA-D7-6527 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-D7-6528         TCGA-D7-6815         TCGA-D7-6817 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-D7-6818         TCGA-D7-6820         TCGA-D7-6822 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-EQ-5647         TCGA-EQ-8122         TCGA-F1-6177 
"16Q GAIN WILD-TYPE"       "16Q GAIN CNV" "16Q GAIN WILD-TYPE" 
        TCGA-F1-6874         TCGA-F1-6875         TCGA-FP-7735 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE"       "16Q GAIN CNV" 
        TCGA-FP-7829         TCGA-FP-7916         TCGA-FP-7998 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-FP-8099         TCGA-FP-8209         TCGA-FP-8210 
      "16Q GAIN CNV" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-FP-8631         TCGA-HJ-7597         TCGA-IN-7806 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-IN-7808         TCGA-IP-7968 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-B7-5816         TCGA-B7-5818         TCGA-BR-6452 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-BR-6455         TCGA-BR-6457         TCGA-BR-6458 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-BR-6563         TCGA-BR-6564         TCGA-BR-6565 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-BR-6566         TCGA-BR-6705         TCGA-BR-6706 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-BR-6707         TCGA-BR-6709         TCGA-BR-6710 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-BR-6801         TCGA-BR-6802         TCGA-BR-6803 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-BR-6852         TCGA-BR-7196         TCGA-BR-7197 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-BR-7703         TCGA-BR-7704         TCGA-BR-7707 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-BR-7715         TCGA-BR-7716         TCGA-BR-7717 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-BR-7722         TCGA-BR-7723         TCGA-BR-7851 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-BR-7901         TCGA-BR-7957         TCGA-BR-7958 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-BR-7959         TCGA-BR-8059         TCGA-BR-8060 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-BR-8077         TCGA-BR-8078         TCGA-BR-8080 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-BR-8081         TCGA-BR-8284         TCGA-BR-8285 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-BR-8286         TCGA-BR-8289         TCGA-BR-8291 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-BR-8295         TCGA-BR-8296         TCGA-BR-8297 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-BR-8592         TCGA-BR-A4IU         TCGA-BR-A4IV 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-BR-A4IY         TCGA-BR-A4IZ         TCGA-BR-A4J1 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-BR-A4J2         TCGA-BR-A4J4         TCGA-BR-A4J5 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-BR-A4J6         TCGA-BR-A4J8         TCGA-BR-A4J9 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-BR-A4PF         TCGA-BR-A4QI         TCGA-BR-A4QL 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-CD-5798         TCGA-CD-5799         TCGA-CD-5800 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-CD-5801         TCGA-CD-5802         TCGA-CD-5803 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-CG-4300         TCGA-CG-4301         TCGA-CG-4304 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-CG-4305         TCGA-CG-4306         TCGA-CG-4436 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-CG-4437         TCGA-CG-4438         TCGA-CG-4440 
"16Q GAIN WILD-TYPE"       "16Q GAIN CNV" "16Q GAIN WILD-TYPE" 
        TCGA-CG-4441         TCGA-CG-4443         TCGA-CG-4444 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-CG-4449         TCGA-CG-4455         TCGA-CG-4460 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE"       "16Q GAIN CNV" 
        TCGA-CG-4462         TCGA-CG-4465         TCGA-CG-4466 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-CG-4469         TCGA-CG-4472         TCGA-CG-4474 
"16Q GAIN WILD-TYPE"       "16Q GAIN CNV" "16Q GAIN WILD-TYPE" 
        TCGA-CG-4477         TCGA-CG-5716         TCGA-CG-5717 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-CG-5718         TCGA-CG-5719         TCGA-CG-5720 
"16Q GAIN WILD-TYPE"       "16Q GAIN CNV" "16Q GAIN WILD-TYPE" 
        TCGA-CG-5721         TCGA-CG-5722         TCGA-CG-5723 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-CG-5724         TCGA-CG-5725         TCGA-CG-5726 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-CG-5727         TCGA-CG-5728         TCGA-CG-5730 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-CG-5732         TCGA-CG-5733         TCGA-CG-5734 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-D7-5577         TCGA-D7-5578         TCGA-D7-5579 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-D7-6518         TCGA-D7-6519         TCGA-D7-6520 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-D7-6521         TCGA-D7-6522         TCGA-D7-6524 
      "16Q GAIN CNV" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-D7-6525         TCGA-D7-6526         TCGA-D7-6527 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-D7-6528         TCGA-D7-6815         TCGA-D7-6817 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-D7-6818         TCGA-D7-6820         TCGA-D7-6822 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-EQ-5647         TCGA-EQ-8122         TCGA-F1-6177 
"16Q GAIN WILD-TYPE"       "16Q GAIN CNV" "16Q GAIN WILD-TYPE" 
        TCGA-F1-6874         TCGA-F1-6875         TCGA-FP-7735 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE"       "16Q GAIN CNV" 
        TCGA-FP-7829         TCGA-FP-7916         TCGA-FP-7998 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-FP-8099         TCGA-FP-8209         TCGA-FP-8210 
      "16Q GAIN CNV" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-FP-8631         TCGA-HJ-7597         TCGA-IN-7806 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-IN-7808         TCGA-IP-7968 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
[1] "hr=" "1.8"
D28V2, continuous
D28V3, binary
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  16Q GAIN CNV          4    6
  16Q GAIN WILD-TYPE   68  102
        clus
vv       16Q GAIN CNV 16Q GAIN WILD-TYPE
  FEMALE            4                 68
  MALE              6                102
                    vv
clus                 STOMACH  ADENOCARCINOMA  DIFFUSE TYPE
  16Q GAIN CNV                                           0
  16Q GAIN WILD-TYPE                                    10
                    vv
clus                 STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  16Q GAIN CNV                                                            1
  16Q GAIN WILD-TYPE                                                     15
                    vv
clus                 STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  16Q GAIN CNV                                                                       1
  16Q GAIN WILD-TYPE                                                                 7
                    vv
clus                 STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE
  16Q GAIN CNV                                                              0
  16Q GAIN WILD-TYPE                                                        3
                    vv
clus                 STOMACH ADENOCARCINOMA  SIGNET RING TYPE
  16Q GAIN CNV                                              0
  16Q GAIN WILD-TYPE                                        1
                    vv
clus                 STOMACH ADENOCARCINOMA - DIFFUSE TYPE
  16Q GAIN CNV                                           1
  16Q GAIN WILD-TYPE                                    15
                    vv
clus                 STOMACH ADENOCARCINOMA - NOT OTHERWISE SPECIFIED (NOS)
  16Q GAIN CNV                                                            3
  16Q GAIN WILD-TYPE                                                     70
                    vv
clus                 STOMACH INTESTINAL ADENOCARCINOMA - MUCINOUS TYPE
  16Q GAIN CNV                                                       0
  16Q GAIN WILD-TYPE                                                 7
                    vv
clus                 STOMACH INTESTINAL ADENOCARCINOMA - PAPILLARY TYPE
  16Q GAIN CNV                                                        0
  16Q GAIN WILD-TYPE                                                  3
                    vv
clus                 STOMACH INTESTINAL ADENOCARCINOMA - TUBULAR TYPE
  16Q GAIN CNV                                                      0
  16Q GAIN WILD-TYPE                                               10
                    vv
clus                 STOMACH INTESTINAL ADENOCARCINOMA - TYPE NOT OTHERWISE SPECIFIED (NOS)
  16Q GAIN CNV                                                                            3
  16Q GAIN WILD-TYPE                                                                     25
D28V4, multiclass
                    vv
clus                 T1 T2 T3 T4
  16Q GAIN CNV        0  2  1  5
  16Q GAIN WILD-TYPE  6 50 55 13
D28V5, multiclass
    clus
vv   16Q GAIN CNV 16Q GAIN WILD-TYPE
  T1            0                  6
  T2            2                 50
  T3            1                 55
  T4            5                 13
                    vv
clus                 N0 N1 N2 N3
  16Q GAIN CNV        2  3  3  0
  16Q GAIN WILD-TYPE 42 46 20 15
D28V6, multiclass
    clus
vv   16Q GAIN CNV 16Q GAIN WILD-TYPE
  N0            2                 42
  N1            3                 46
  N2            3                 20
  N3            0                 15
                    vv
clus                  M0  M1  MX
  16Q GAIN CNV         5   2   1
  16Q GAIN WILD-TYPE 113  14   7
D28V7, multiclass
    clus
vv   16Q GAIN CNV 16Q GAIN WILD-TYPE
  M0            5                113
  M1            2                 14
  MX            1                  7
                    vv
clus                  I II III IV
  16Q GAIN CNV        1  0   2  5
  16Q GAIN WILD-TYPE 23 37  37 21
D28V8, multiclass
     clus
vv    16Q GAIN CNV 16Q GAIN WILD-TYPE
  I              1                 23
  II             0                 37
  III            2                 37
  IV             5                 21
D28V9, binary
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  16Q GAIN CNV          0   10
  16Q GAIN WILD-TYPE    5  165
     clus
vv    16Q GAIN CNV 16Q GAIN WILD-TYPE
  NO             0                  5
  YES           10                165
                    vv
clus                  R0  R1  R2  RX
  16Q GAIN CNV         7   0   1   1
  16Q GAIN WILD-TYPE 118   7  11  24
D28V10, multiclass
    clus
vv   16Q GAIN CNV 16Q GAIN WILD-TYPE
  R0            7                118
  R1            0                  7
  R2            1                 11
  RX            1                 24
D28V11, continuous

Clustering(29) Variable = 17p gain
D29V1, survival
                    sevent
clus2                  0   1
  17P GAIN CNV         3   3
  17P GAIN WILD-TYPE 121  16
      17P GAIN CNV 17P GAIN WILD-TYPE 
                 6                137 
      17P GAIN CNV 17P GAIN WILD-TYPE 
                 3                 16 
$`17P GAIN CNV`
TCGA-BR-A4QI TCGA-CG-4460 TCGA-CG-5724 TCGA-D7-6817 TCGA-EQ-5647 TCGA-FP-7829 
        0.49        21.99        12.03         4.70         0.62         0.20 

$`17P GAIN WILD-TYPE`
TCGA-B7-5816 TCGA-B7-5818 TCGA-BR-6452 TCGA-BR-6455 TCGA-BR-6457 TCGA-BR-6458 
        5.62         0.10         0.95         1.41         1.35         1.35 
TCGA-BR-6563 TCGA-BR-6564 TCGA-BR-6565 TCGA-BR-6566 TCGA-BR-6705 TCGA-BR-6706 
        0.85         0.82         0.62         0.62         1.71         2.17 
TCGA-BR-6707 TCGA-BR-6709 TCGA-BR-6710 TCGA-BR-6801 TCGA-BR-6802 TCGA-BR-6803 
        0.99         1.22         0.66         1.12         0.76         0.66 
TCGA-BR-6852 TCGA-BR-7196 TCGA-BR-7197 TCGA-BR-7703 TCGA-BR-7704 TCGA-BR-7707 
        0.26         1.22         1.48         0.46         1.25         0.13 
TCGA-BR-7715 TCGA-BR-7716 TCGA-BR-7717 TCGA-BR-7722 TCGA-BR-7723 TCGA-BR-7851 
        1.05         0.82         0.69         0.16         4.54         0.99 
TCGA-BR-7901 TCGA-BR-7957 TCGA-BR-7958 TCGA-BR-7959 TCGA-BR-8059 TCGA-BR-8060 
        0.95         0.69         0.16         1.08         0.82         1.32 
TCGA-BR-8077 TCGA-BR-8078 TCGA-BR-8080 TCGA-BR-8081 TCGA-BR-8284 TCGA-BR-8285 
        0.69         0.95         0.49         0.46         0.72         0.26 
TCGA-BR-8286 TCGA-BR-8289 TCGA-BR-8291 TCGA-BR-8295 TCGA-BR-8296 TCGA-BR-8297 
        0.43         0.26         1.18         1.55         1.48         0.76 
TCGA-BR-8592 TCGA-BR-A4IU TCGA-BR-A4IV TCGA-BR-A4IY TCGA-BR-A4IZ TCGA-BR-A4J1 
        0.20         0.59         0.92         0.39         0.79         0.72 
TCGA-BR-A4J2 TCGA-BR-A4J4 TCGA-BR-A4J5 TCGA-BR-A4J6 TCGA-BR-A4J8 TCGA-BR-A4J9 
        0.79         0.53         0.43         0.13         0.23         0.10 
TCGA-BR-A4PF TCGA-BR-A4QL TCGA-CD-5798 TCGA-CD-5799 TCGA-CD-5800 TCGA-CD-5801 
        0.72         2.24         0.82         0.69         0.36         0.49 
TCGA-CD-5802 TCGA-CD-5803 TCGA-CG-4300 TCGA-CG-4301 TCGA-CG-4304 TCGA-CG-4305 
        0.30         0.07        20.02         3.02        27.02        15.95 
TCGA-CG-4306 TCGA-CG-4436 TCGA-CG-4437 TCGA-CG-4438 TCGA-CG-4440 TCGA-CG-4441 
        1.02        52.96         8.05        54.05         4.01        14.01 
TCGA-CG-4443 TCGA-CG-4444 TCGA-CG-4449 TCGA-CG-4455 TCGA-CG-4462 TCGA-CG-4465 
       29.98        47.05        19.07        12.03         1.02         8.98 
TCGA-CG-4466 TCGA-CG-4469 TCGA-CG-4472 TCGA-CG-4474 TCGA-CG-4477 TCGA-CG-5716 
       18.94         7.07        12.00         1.02         1.02         1.02 
TCGA-CG-5717 TCGA-CG-5718 TCGA-CG-5719 TCGA-CG-5720 TCGA-CG-5721 TCGA-CG-5722 
        6.94         1.02         1.02         0.99         5.98         0.95 
TCGA-CG-5723 TCGA-CG-5725 TCGA-CG-5726 TCGA-CG-5727 TCGA-CG-5728 TCGA-CG-5730 
       70.06        15.02        28.96        31.04        65.10         4.01 
TCGA-CG-5732 TCGA-CG-5733 TCGA-CG-5734 TCGA-D7-5577 TCGA-D7-5578 TCGA-D7-5579 
       55.04        21.07         7.99         8.65         3.58         4.54 
TCGA-D7-6518 TCGA-D7-6519 TCGA-D7-6520 TCGA-D7-6521 TCGA-D7-6522 TCGA-D7-6524 
        9.80        15.65         9.63         8.19         6.90         0.69 
TCGA-D7-6525 TCGA-D7-6526 TCGA-D7-6527 TCGA-D7-6528 TCGA-D7-6815 TCGA-D7-6818 
        5.95         6.61         4.14         1.68         3.65         4.04 
TCGA-D7-6820 TCGA-D7-6822 TCGA-EQ-8122 TCGA-F1-6177 TCGA-F1-6874 TCGA-F1-6875 
        2.93         4.27         7.79         6.54         2.01        72.23 
TCGA-FP-7735 TCGA-FP-7916 TCGA-FP-7998 TCGA-FP-8099 TCGA-FP-8209 TCGA-FP-8210 
        0.39         3.02         3.58         1.02        59.05         5.03 
TCGA-FP-8631 TCGA-HJ-7597 TCGA-IN-7806 TCGA-IN-7808 TCGA-IP-7968 
        0.56        26.43         6.87         3.55         2.53 

      17P GAIN CNV 17P GAIN WILD-TYPE 
              0.20               0.07 
      17P GAIN CNV 17P GAIN WILD-TYPE 
             21.99              72.23 
      17P GAIN CNV 17P GAIN WILD-TYPE 
              2.66               1.25 
[1] "0.2 - 22.0 (2.7)" "0.1 - 72.2 (1.2)"
        TCGA-B7-5816         TCGA-B7-5818         TCGA-BR-6452 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-BR-6455         TCGA-BR-6457         TCGA-BR-6458 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-BR-6563         TCGA-BR-6564         TCGA-BR-6565 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-BR-6566         TCGA-BR-6705         TCGA-BR-6706 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-BR-6707         TCGA-BR-6709         TCGA-BR-6710 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-BR-6801         TCGA-BR-6802         TCGA-BR-6803 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-BR-6852         TCGA-BR-7196         TCGA-BR-7197 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-BR-7703         TCGA-BR-7704         TCGA-BR-7707 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-BR-7715         TCGA-BR-7716         TCGA-BR-7717 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-BR-7722         TCGA-BR-7723         TCGA-BR-7851 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-BR-7901         TCGA-BR-7957         TCGA-BR-7958 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-BR-7959         TCGA-BR-8059         TCGA-BR-8060 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-BR-8077         TCGA-BR-8078         TCGA-BR-8080 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-BR-8081         TCGA-BR-8284         TCGA-BR-8285 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-BR-8286         TCGA-BR-8289         TCGA-BR-8291 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-BR-8295         TCGA-BR-8296         TCGA-BR-8297 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-BR-8592         TCGA-BR-A4IU         TCGA-BR-A4IV 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-BR-A4IY         TCGA-BR-A4IZ         TCGA-BR-A4J1 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-BR-A4J2         TCGA-BR-A4J4         TCGA-BR-A4J5 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-BR-A4J6         TCGA-BR-A4J8         TCGA-BR-A4J9 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-BR-A4PF         TCGA-BR-A4QI         TCGA-BR-A4QL 
"17P GAIN WILD-TYPE"       "17P GAIN CNV" "17P GAIN WILD-TYPE" 
        TCGA-CD-5798         TCGA-CD-5799         TCGA-CD-5800 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-CD-5801         TCGA-CD-5802         TCGA-CD-5803 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-CG-4300         TCGA-CG-4301         TCGA-CG-4304 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-CG-4305         TCGA-CG-4306         TCGA-CG-4436 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-CG-4437         TCGA-CG-4438         TCGA-CG-4440 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-CG-4441         TCGA-CG-4443         TCGA-CG-4444 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-CG-4449         TCGA-CG-4455         TCGA-CG-4460 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE"       "17P GAIN CNV" 
        TCGA-CG-4462         TCGA-CG-4465         TCGA-CG-4466 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-CG-4469         TCGA-CG-4472         TCGA-CG-4474 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-CG-4477         TCGA-CG-5716         TCGA-CG-5717 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-CG-5718         TCGA-CG-5719         TCGA-CG-5720 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-CG-5721         TCGA-CG-5722         TCGA-CG-5723 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-CG-5724         TCGA-CG-5725         TCGA-CG-5726 
      "17P GAIN CNV" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-CG-5727         TCGA-CG-5728         TCGA-CG-5730 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-CG-5732         TCGA-CG-5733         TCGA-CG-5734 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-D7-5577         TCGA-D7-5578         TCGA-D7-5579 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-D7-6518         TCGA-D7-6519         TCGA-D7-6520 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-D7-6521         TCGA-D7-6522         TCGA-D7-6524 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-D7-6525         TCGA-D7-6526         TCGA-D7-6527 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-D7-6528         TCGA-D7-6815         TCGA-D7-6817 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE"       "17P GAIN CNV" 
        TCGA-D7-6818         TCGA-D7-6820         TCGA-D7-6822 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-EQ-5647         TCGA-EQ-8122         TCGA-F1-6177 
      "17P GAIN CNV" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-F1-6874         TCGA-F1-6875         TCGA-FP-7735 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-FP-7829         TCGA-FP-7916         TCGA-FP-7998 
      "17P GAIN CNV" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-FP-8099         TCGA-FP-8209         TCGA-FP-8210 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-FP-8631         TCGA-HJ-7597         TCGA-IN-7806 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-IN-7808         TCGA-IP-7968 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-B7-5816         TCGA-B7-5818         TCGA-BR-6452 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-BR-6455         TCGA-BR-6457         TCGA-BR-6458 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-BR-6563         TCGA-BR-6564         TCGA-BR-6565 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-BR-6566         TCGA-BR-6705         TCGA-BR-6706 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-BR-6707         TCGA-BR-6709         TCGA-BR-6710 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-BR-6801         TCGA-BR-6802         TCGA-BR-6803 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-BR-6852         TCGA-BR-7196         TCGA-BR-7197 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-BR-7703         TCGA-BR-7704         TCGA-BR-7707 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-BR-7715         TCGA-BR-7716         TCGA-BR-7717 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-BR-7722         TCGA-BR-7723         TCGA-BR-7851 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-BR-7901         TCGA-BR-7957         TCGA-BR-7958 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-BR-7959         TCGA-BR-8059         TCGA-BR-8060 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-BR-8077         TCGA-BR-8078         TCGA-BR-8080 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-BR-8081         TCGA-BR-8284         TCGA-BR-8285 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-BR-8286         TCGA-BR-8289         TCGA-BR-8291 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-BR-8295         TCGA-BR-8296         TCGA-BR-8297 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-BR-8592         TCGA-BR-A4IU         TCGA-BR-A4IV 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-BR-A4IY         TCGA-BR-A4IZ         TCGA-BR-A4J1 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-BR-A4J2         TCGA-BR-A4J4         TCGA-BR-A4J5 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-BR-A4J6         TCGA-BR-A4J8         TCGA-BR-A4J9 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-BR-A4PF         TCGA-BR-A4QI         TCGA-BR-A4QL 
"17P GAIN WILD-TYPE"       "17P GAIN CNV" "17P GAIN WILD-TYPE" 
        TCGA-CD-5798         TCGA-CD-5799         TCGA-CD-5800 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-CD-5801         TCGA-CD-5802         TCGA-CD-5803 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-CG-4300         TCGA-CG-4301         TCGA-CG-4304 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-CG-4305         TCGA-CG-4306         TCGA-CG-4436 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-CG-4437         TCGA-CG-4438         TCGA-CG-4440 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-CG-4441         TCGA-CG-4443         TCGA-CG-4444 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-CG-4449         TCGA-CG-4455         TCGA-CG-4460 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE"       "17P GAIN CNV" 
        TCGA-CG-4462         TCGA-CG-4465         TCGA-CG-4466 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-CG-4469         TCGA-CG-4472         TCGA-CG-4474 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-CG-4477         TCGA-CG-5716         TCGA-CG-5717 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-CG-5718         TCGA-CG-5719         TCGA-CG-5720 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-CG-5721         TCGA-CG-5722         TCGA-CG-5723 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-CG-5724         TCGA-CG-5725         TCGA-CG-5726 
      "17P GAIN CNV" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-CG-5727         TCGA-CG-5728         TCGA-CG-5730 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-CG-5732         TCGA-CG-5733         TCGA-CG-5734 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-D7-5577         TCGA-D7-5578         TCGA-D7-5579 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-D7-6518         TCGA-D7-6519         TCGA-D7-6520 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-D7-6521         TCGA-D7-6522         TCGA-D7-6524 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-D7-6525         TCGA-D7-6526         TCGA-D7-6527 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-D7-6528         TCGA-D7-6815         TCGA-D7-6817 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE"       "17P GAIN CNV" 
        TCGA-D7-6818         TCGA-D7-6820         TCGA-D7-6822 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-EQ-5647         TCGA-EQ-8122         TCGA-F1-6177 
      "17P GAIN CNV" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-F1-6874         TCGA-F1-6875         TCGA-FP-7735 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-FP-7829         TCGA-FP-7916         TCGA-FP-7998 
      "17P GAIN CNV" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-FP-8099         TCGA-FP-8209         TCGA-FP-8210 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-FP-8631         TCGA-HJ-7597         TCGA-IN-7806 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-IN-7808         TCGA-IP-7968 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-B7-5816         TCGA-B7-5818         TCGA-BR-6452 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-BR-6455         TCGA-BR-6457         TCGA-BR-6458 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-BR-6563         TCGA-BR-6564         TCGA-BR-6565 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-BR-6566         TCGA-BR-6705         TCGA-BR-6706 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-BR-6707         TCGA-BR-6709         TCGA-BR-6710 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-BR-6801         TCGA-BR-6802         TCGA-BR-6803 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-BR-6852         TCGA-BR-7196         TCGA-BR-7197 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-BR-7703         TCGA-BR-7704         TCGA-BR-7707 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-BR-7715         TCGA-BR-7716         TCGA-BR-7717 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-BR-7722         TCGA-BR-7723         TCGA-BR-7851 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-BR-7901         TCGA-BR-7957         TCGA-BR-7958 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-BR-7959         TCGA-BR-8059         TCGA-BR-8060 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-BR-8077         TCGA-BR-8078         TCGA-BR-8080 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-BR-8081         TCGA-BR-8284         TCGA-BR-8285 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-BR-8286         TCGA-BR-8289         TCGA-BR-8291 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-BR-8295         TCGA-BR-8296         TCGA-BR-8297 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-BR-8592         TCGA-BR-A4IU         TCGA-BR-A4IV 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-BR-A4IY         TCGA-BR-A4IZ         TCGA-BR-A4J1 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-BR-A4J2         TCGA-BR-A4J4         TCGA-BR-A4J5 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-BR-A4J6         TCGA-BR-A4J8         TCGA-BR-A4J9 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-BR-A4PF         TCGA-BR-A4QI         TCGA-BR-A4QL 
"17P GAIN WILD-TYPE"       "17P GAIN CNV" "17P GAIN WILD-TYPE" 
        TCGA-CD-5798         TCGA-CD-5799         TCGA-CD-5800 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-CD-5801         TCGA-CD-5802         TCGA-CD-5803 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-CG-4300         TCGA-CG-4301         TCGA-CG-4304 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-CG-4305         TCGA-CG-4306         TCGA-CG-4436 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-CG-4437         TCGA-CG-4438         TCGA-CG-4440 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-CG-4441         TCGA-CG-4443         TCGA-CG-4444 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-CG-4449         TCGA-CG-4455         TCGA-CG-4460 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE"       "17P GAIN CNV" 
        TCGA-CG-4462         TCGA-CG-4465         TCGA-CG-4466 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-CG-4469         TCGA-CG-4472         TCGA-CG-4474 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-CG-4477         TCGA-CG-5716         TCGA-CG-5717 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-CG-5718         TCGA-CG-5719         TCGA-CG-5720 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-CG-5721         TCGA-CG-5722         TCGA-CG-5723 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-CG-5724         TCGA-CG-5725         TCGA-CG-5726 
      "17P GAIN CNV" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-CG-5727         TCGA-CG-5728         TCGA-CG-5730 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-CG-5732         TCGA-CG-5733         TCGA-CG-5734 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-D7-5577         TCGA-D7-5578         TCGA-D7-5579 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-D7-6518         TCGA-D7-6519         TCGA-D7-6520 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-D7-6521         TCGA-D7-6522         TCGA-D7-6524 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-D7-6525         TCGA-D7-6526         TCGA-D7-6527 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-D7-6528         TCGA-D7-6815         TCGA-D7-6817 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE"       "17P GAIN CNV" 
        TCGA-D7-6818         TCGA-D7-6820         TCGA-D7-6822 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-EQ-5647         TCGA-EQ-8122         TCGA-F1-6177 
      "17P GAIN CNV" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-F1-6874         TCGA-F1-6875         TCGA-FP-7735 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-FP-7829         TCGA-FP-7916         TCGA-FP-7998 
      "17P GAIN CNV" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-FP-8099         TCGA-FP-8209         TCGA-FP-8210 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-FP-8631         TCGA-HJ-7597         TCGA-IN-7806 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-IN-7808         TCGA-IP-7968 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
[1] "hr=" "4.5"
D29V2, continuous
D29V3, binary
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  17P GAIN CNV          3    3
  17P GAIN WILD-TYPE   69  105
        clus
vv       17P GAIN CNV 17P GAIN WILD-TYPE
  FEMALE            3                 69
  MALE              3                105
                    vv
clus                 STOMACH  ADENOCARCINOMA  DIFFUSE TYPE
  17P GAIN CNV                                           0
  17P GAIN WILD-TYPE                                    10
                    vv
clus                 STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  17P GAIN CNV                                                            1
  17P GAIN WILD-TYPE                                                     15
                    vv
clus                 STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  17P GAIN CNV                                                                       0
  17P GAIN WILD-TYPE                                                                 8
                    vv
clus                 STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE
  17P GAIN CNV                                                              0
  17P GAIN WILD-TYPE                                                        3
                    vv
clus                 STOMACH ADENOCARCINOMA  SIGNET RING TYPE
  17P GAIN CNV                                              0
  17P GAIN WILD-TYPE                                        1
                    vv
clus                 STOMACH ADENOCARCINOMA - DIFFUSE TYPE
  17P GAIN CNV                                           1
  17P GAIN WILD-TYPE                                    15
                    vv
clus                 STOMACH ADENOCARCINOMA - NOT OTHERWISE SPECIFIED (NOS)
  17P GAIN CNV                                                            1
  17P GAIN WILD-TYPE                                                     72
                    vv
clus                 STOMACH INTESTINAL ADENOCARCINOMA - MUCINOUS TYPE
  17P GAIN CNV                                                       1
  17P GAIN WILD-TYPE                                                 6
                    vv
clus                 STOMACH INTESTINAL ADENOCARCINOMA - PAPILLARY TYPE
  17P GAIN CNV                                                        0
  17P GAIN WILD-TYPE                                                  3
                    vv
clus                 STOMACH INTESTINAL ADENOCARCINOMA - TUBULAR TYPE
  17P GAIN CNV                                                      1
  17P GAIN WILD-TYPE                                                9
                    vv
clus                 STOMACH INTESTINAL ADENOCARCINOMA - TYPE NOT OTHERWISE SPECIFIED (NOS)
  17P GAIN CNV                                                                            1
  17P GAIN WILD-TYPE                                                                     27
D29V4, multiclass
                    vv
clus                 T1 T2 T3 T4
  17P GAIN CNV        0  1  2  2
  17P GAIN WILD-TYPE  6 51 54 16
D29V5, multiclass
    clus
vv   17P GAIN CNV 17P GAIN WILD-TYPE
  T1            0                  6
  T2            1                 51
  T3            2                 54
  T4            2                 16
                    vv
clus                 N0 N1 N2 N3
  17P GAIN CNV        0  2  0  3
  17P GAIN WILD-TYPE 44 47 23 12
D29V6, multiclass
    clus
vv   17P GAIN CNV 17P GAIN WILD-TYPE
  N0            0                 44
  N1            2                 47
  N2            0                 23
  N3            3                 12
                    vv
clus                  M0  M1  MX
  17P GAIN CNV         2   3   0
  17P GAIN WILD-TYPE 116  13   8
D29V7, multiclass
    clus
vv   17P GAIN CNV 17P GAIN WILD-TYPE
  M0            2                116
  M1            3                 13
  MX            0                  8
                    vv
clus                  I II III IV
  17P GAIN CNV        0  0   2  3
  17P GAIN WILD-TYPE 24 37  37 23
D29V8, multiclass
     clus
vv    17P GAIN CNV 17P GAIN WILD-TYPE
  I              0                 24
  II             0                 37
  III            2                 37
  IV             3                 23
D29V9, binary
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  17P GAIN CNV          0    6
  17P GAIN WILD-TYPE    5  169
     clus
vv    17P GAIN CNV 17P GAIN WILD-TYPE
  NO             0                  5
  YES            6                169
                    vv
clus                  R0  R1  R2  RX
  17P GAIN CNV         3   0   3   0
  17P GAIN WILD-TYPE 122   7   9  25
D29V10, multiclass
    clus
vv   17P GAIN CNV 17P GAIN WILD-TYPE
  R0            3                122
  R1            0                  7
  R2            3                  9
  RX            0                 25
D29V11, continuous

Clustering(30) Variable = 17q gain
D30V1, survival
                    sevent
clus2                  0   1
  17Q GAIN CNV         7   4
  17Q GAIN WILD-TYPE 117  15
      17Q GAIN CNV 17Q GAIN WILD-TYPE 
                11                132 
      17Q GAIN CNV 17Q GAIN WILD-TYPE 
                 4                 15 
$`17Q GAIN CNV`
TCGA-B7-5818 TCGA-BR-8289 TCGA-BR-A4J4 TCGA-BR-A4QI TCGA-CG-4460 TCGA-CG-5719 
        0.10         0.26         0.53         0.49        21.99         1.02 
TCGA-CG-5724 TCGA-D7-6817 TCGA-EQ-5647 TCGA-F1-6875 TCGA-FP-7829 
       12.03         4.70         0.62        72.23         0.20 

$`17Q GAIN WILD-TYPE`
TCGA-B7-5816 TCGA-BR-6452 TCGA-BR-6455 TCGA-BR-6457 TCGA-BR-6458 TCGA-BR-6563 
        5.62         0.95         1.41         1.35         1.35         0.85 
TCGA-BR-6564 TCGA-BR-6565 TCGA-BR-6566 TCGA-BR-6705 TCGA-BR-6706 TCGA-BR-6707 
        0.82         0.62         0.62         1.71         2.17         0.99 
TCGA-BR-6709 TCGA-BR-6710 TCGA-BR-6801 TCGA-BR-6802 TCGA-BR-6803 TCGA-BR-6852 
        1.22         0.66         1.12         0.76         0.66         0.26 
TCGA-BR-7196 TCGA-BR-7197 TCGA-BR-7703 TCGA-BR-7704 TCGA-BR-7707 TCGA-BR-7715 
        1.22         1.48         0.46         1.25         0.13         1.05 
TCGA-BR-7716 TCGA-BR-7717 TCGA-BR-7722 TCGA-BR-7723 TCGA-BR-7851 TCGA-BR-7901 
        0.82         0.69         0.16         4.54         0.99         0.95 
TCGA-BR-7957 TCGA-BR-7958 TCGA-BR-7959 TCGA-BR-8059 TCGA-BR-8060 TCGA-BR-8077 
        0.69         0.16         1.08         0.82         1.32         0.69 
TCGA-BR-8078 TCGA-BR-8080 TCGA-BR-8081 TCGA-BR-8284 TCGA-BR-8285 TCGA-BR-8286 
        0.95         0.49         0.46         0.72         0.26         0.43 
TCGA-BR-8291 TCGA-BR-8295 TCGA-BR-8296 TCGA-BR-8297 TCGA-BR-8592 TCGA-BR-A4IU 
        1.18         1.55         1.48         0.76         0.20         0.59 
TCGA-BR-A4IV TCGA-BR-A4IY TCGA-BR-A4IZ TCGA-BR-A4J1 TCGA-BR-A4J2 TCGA-BR-A4J5 
        0.92         0.39         0.79         0.72         0.79         0.43 
TCGA-BR-A4J6 TCGA-BR-A4J8 TCGA-BR-A4J9 TCGA-BR-A4PF TCGA-BR-A4QL TCGA-CD-5798 
        0.13         0.23         0.10         0.72         2.24         0.82 
TCGA-CD-5799 TCGA-CD-5800 TCGA-CD-5801 TCGA-CD-5802 TCGA-CD-5803 TCGA-CG-4300 
        0.69         0.36         0.49         0.30         0.07        20.02 
TCGA-CG-4301 TCGA-CG-4304 TCGA-CG-4305 TCGA-CG-4306 TCGA-CG-4436 TCGA-CG-4437 
        3.02        27.02        15.95         1.02        52.96         8.05 
TCGA-CG-4438 TCGA-CG-4440 TCGA-CG-4441 TCGA-CG-4443 TCGA-CG-4444 TCGA-CG-4449 
       54.05         4.01        14.01        29.98        47.05        19.07 
TCGA-CG-4455 TCGA-CG-4462 TCGA-CG-4465 TCGA-CG-4466 TCGA-CG-4469 TCGA-CG-4472 
       12.03         1.02         8.98        18.94         7.07        12.00 
TCGA-CG-4474 TCGA-CG-4477 TCGA-CG-5716 TCGA-CG-5717 TCGA-CG-5718 TCGA-CG-5720 
        1.02         1.02         1.02         6.94         1.02         0.99 
TCGA-CG-5721 TCGA-CG-5722 TCGA-CG-5723 TCGA-CG-5725 TCGA-CG-5726 TCGA-CG-5727 
        5.98         0.95        70.06        15.02        28.96        31.04 
TCGA-CG-5728 TCGA-CG-5730 TCGA-CG-5732 TCGA-CG-5733 TCGA-CG-5734 TCGA-D7-5577 
       65.10         4.01        55.04        21.07         7.99         8.65 
TCGA-D7-5578 TCGA-D7-5579 TCGA-D7-6518 TCGA-D7-6519 TCGA-D7-6520 TCGA-D7-6521 
        3.58         4.54         9.80        15.65         9.63         8.19 
TCGA-D7-6522 TCGA-D7-6524 TCGA-D7-6525 TCGA-D7-6526 TCGA-D7-6527 TCGA-D7-6528 
        6.90         0.69         5.95         6.61         4.14         1.68 
TCGA-D7-6815 TCGA-D7-6818 TCGA-D7-6820 TCGA-D7-6822 TCGA-EQ-8122 TCGA-F1-6177 
        3.65         4.04         2.93         4.27         7.79         6.54 
TCGA-F1-6874 TCGA-FP-7735 TCGA-FP-7916 TCGA-FP-7998 TCGA-FP-8099 TCGA-FP-8209 
        2.01         0.39         3.02         3.58         1.02        59.05 
TCGA-FP-8210 TCGA-FP-8631 TCGA-HJ-7597 TCGA-IN-7806 TCGA-IN-7808 TCGA-IP-7968 
        5.03         0.56        26.43         6.87         3.55         2.53 

      17Q GAIN CNV 17Q GAIN WILD-TYPE 
              0.10               0.07 
      17Q GAIN CNV 17Q GAIN WILD-TYPE 
             72.23              70.06 
      17Q GAIN CNV 17Q GAIN WILD-TYPE 
             0.620              1.335 
[1] "0.1 - 72.2 (0.6)" "0.1 - 70.1 (1.3)"
        TCGA-B7-5816         TCGA-B7-5818         TCGA-BR-6452 
"17Q GAIN WILD-TYPE"       "17Q GAIN CNV" "17Q GAIN WILD-TYPE" 
        TCGA-BR-6455         TCGA-BR-6457         TCGA-BR-6458 
"17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" 
        TCGA-BR-6563         TCGA-BR-6564         TCGA-BR-6565 
"17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" 
        TCGA-BR-6566         TCGA-BR-6705         TCGA-BR-6706 
"17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" 
        TCGA-BR-6707         TCGA-BR-6709         TCGA-BR-6710 
"17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" 
        TCGA-BR-6801         TCGA-BR-6802         TCGA-BR-6803 
"17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" 
        TCGA-BR-6852         TCGA-BR-7196         TCGA-BR-7197 
"17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" 
        TCGA-BR-7703         TCGA-BR-7704         TCGA-BR-7707 
"17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" 
        TCGA-BR-7715         TCGA-BR-7716         TCGA-BR-7717 
"17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" 
        TCGA-BR-7722         TCGA-BR-7723         TCGA-BR-7851 
"17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" 
        TCGA-BR-7901         TCGA-BR-7957         TCGA-BR-7958 
"17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" 
        TCGA-BR-7959         TCGA-BR-8059         TCGA-BR-8060 
"17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" 
        TCGA-BR-8077         TCGA-BR-8078         TCGA-BR-8080 
"17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" 
        TCGA-BR-8081         TCGA-BR-8284         TCGA-BR-8285 
"17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" 
        TCGA-BR-8286         TCGA-BR-8289         TCGA-BR-8291 
"17Q GAIN WILD-TYPE"       "17Q GAIN CNV" "17Q GAIN WILD-TYPE" 
        TCGA-BR-8295         TCGA-BR-8296         TCGA-BR-8297 
"17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" 
        TCGA-BR-8592         TCGA-BR-A4IU         TCGA-BR-A4IV 
"17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" 
        TCGA-BR-A4IY         TCGA-BR-A4IZ         TCGA-BR-A4J1 
"17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" 
        TCGA-BR-A4J2         TCGA-BR-A4J4         TCGA-BR-A4J5 
"17Q GAIN WILD-TYPE"       "17Q GAIN CNV" "17Q GAIN WILD-TYPE" 
        TCGA-BR-A4J6         TCGA-BR-A4J8         TCGA-BR-A4J9 
"17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" 
        TCGA-BR-A4PF         TCGA-BR-A4QI         TCGA-BR-A4QL 
"17Q GAIN WILD-TYPE"       "17Q GAIN CNV" "17Q GAIN WILD-TYPE" 
        TCGA-CD-5798         TCGA-CD-5799         TCGA-CD-5800 
"17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" 
        TCGA-CD-5801         TCGA-CD-5802         TCGA-CD-5803 
"17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" 
        TCGA-CG-4300         TCGA-CG-4301         TCGA-CG-4304 
"17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" 
        TCGA-CG-4305         TCGA-CG-4306         TCGA-CG-4436 
"17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" 
        TCGA-CG-4437         TCGA-CG-4438         TCGA-CG-4440 
"17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" 
        TCGA-CG-4441         TCGA-CG-4443         TCGA-CG-4444 
"17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" 
        TCGA-CG-4449         TCGA-CG-4455         TCGA-CG-4460 
"17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE"       "17Q GAIN CNV" 
        TCGA-CG-4462         TCGA-CG-4465         TCGA-CG-4466 
"17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" 
        TCGA-CG-4469         TCGA-CG-4472         TCGA-CG-4474 
"17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" 
        TCGA-CG-4477         TCGA-CG-5716         TCGA-CG-5717 
"17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" 
        TCGA-CG-5718         TCGA-CG-5719         TCGA-CG-5720 
"17Q GAIN WILD-TYPE"       "17Q GAIN CNV" "17Q GAIN WILD-TYPE" 
        TCGA-CG-5721         TCGA-CG-5722         TCGA-CG-5723 
"17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" 
        TCGA-CG-5724         TCGA-CG-5725         TCGA-CG-5726 
      "17Q GAIN CNV" "17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" 
        TCGA-CG-5727         TCGA-CG-5728         TCGA-CG-5730 
"17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" 
        TCGA-CG-5732         TCGA-CG-5733         TCGA-CG-5734 
"17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" 
        TCGA-D7-5577         TCGA-D7-5578         TCGA-D7-5579 
"17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" 
        TCGA-D7-6518         TCGA-D7-6519         TCGA-D7-6520 
"17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" 
        TCGA-D7-6521         TCGA-D7-6522         TCGA-D7-6524 
"17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" 
        TCGA-D7-6525         TCGA-D7-6526         TCGA-D7-6527 
"17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" 
        TCGA-D7-6528         TCGA-D7-6815         TCGA-D7-6817 
"17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE"       "17Q GAIN CNV" 
        TCGA-D7-6818         TCGA-D7-6820         TCGA-D7-6822 
"17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" 
        TCGA-EQ-5647         TCGA-EQ-8122         TCGA-F1-6177 
      "17Q GAIN CNV" "17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" 
        TCGA-F1-6874         TCGA-F1-6875         TCGA-FP-7735 
"17Q GAIN WILD-TYPE"       "17Q GAIN CNV" "17Q GAIN WILD-TYPE" 
        TCGA-FP-7829         TCGA-FP-7916         TCGA-FP-7998 
      "17Q GAIN CNV" "17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" 
        TCGA-FP-8099         TCGA-FP-8209         TCGA-FP-8210 
"17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" 
        TCGA-FP-8631         TCGA-HJ-7597         TCGA-IN-7806 
"17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" 
        TCGA-IN-7808         TCGA-IP-7968 
"17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" 
        TCGA-B7-5816         TCGA-B7-5818         TCGA-BR-6452 
"17Q GAIN WILD-TYPE"       "17Q GAIN CNV" "17Q GAIN WILD-TYPE" 
        TCGA-BR-6455         TCGA-BR-6457         TCGA-BR-6458 
"17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" 
        TCGA-BR-6563         TCGA-BR-6564         TCGA-BR-6565 
"17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" 
        TCGA-BR-6566         TCGA-BR-6705         TCGA-BR-6706 
"17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" 
        TCGA-BR-6707         TCGA-BR-6709         TCGA-BR-6710 
"17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" 
        TCGA-BR-6801         TCGA-BR-6802         TCGA-BR-6803 
"17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" 
        TCGA-BR-6852         TCGA-BR-7196         TCGA-BR-7197 
"17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" 
        TCGA-BR-7703         TCGA-BR-7704         TCGA-BR-7707 
"17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" 
        TCGA-BR-7715         TCGA-BR-7716         TCGA-BR-7717 
"17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" 
        TCGA-BR-7722         TCGA-BR-7723         TCGA-BR-7851 
"17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" 
        TCGA-BR-7901         TCGA-BR-7957         TCGA-BR-7958 
"17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" 
        TCGA-BR-7959         TCGA-BR-8059         TCGA-BR-8060 
"17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" 
        TCGA-BR-8077         TCGA-BR-8078         TCGA-BR-8080 
"17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" 
        TCGA-BR-8081         TCGA-BR-8284         TCGA-BR-8285 
"17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" 
        TCGA-BR-8286         TCGA-BR-8289         TCGA-BR-8291 
"17Q GAIN WILD-TYPE"       "17Q GAIN CNV" "17Q GAIN WILD-TYPE" 
        TCGA-BR-8295         TCGA-BR-8296         TCGA-BR-8297 
"17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" 
        TCGA-BR-8592         TCGA-BR-A4IU         TCGA-BR-A4IV 
"17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" 
        TCGA-BR-A4IY         TCGA-BR-A4IZ         TCGA-BR-A4J1 
"17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" 
        TCGA-BR-A4J2         TCGA-BR-A4J4         TCGA-BR-A4J5 
"17Q GAIN WILD-TYPE"       "17Q GAIN CNV" "17Q GAIN WILD-TYPE" 
        TCGA-BR-A4J6         TCGA-BR-A4J8         TCGA-BR-A4J9 
"17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" 
        TCGA-BR-A4PF         TCGA-BR-A4QI         TCGA-BR-A4QL 
"17Q GAIN WILD-TYPE"       "17Q GAIN CNV" "17Q GAIN WILD-TYPE" 
        TCGA-CD-5798         TCGA-CD-5799         TCGA-CD-5800 
"17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" 
        TCGA-CD-5801         TCGA-CD-5802         TCGA-CD-5803 
"17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" 
        TCGA-CG-4300         TCGA-CG-4301         TCGA-CG-4304 
"17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" 
        TCGA-CG-4305         TCGA-CG-4306         TCGA-CG-4436 
"17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" 
        TCGA-CG-4437         TCGA-CG-4438         TCGA-CG-4440 
"17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" 
        TCGA-CG-4441         TCGA-CG-4443         TCGA-CG-4444 
"17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" 
        TCGA-CG-4449         TCGA-CG-4455         TCGA-CG-4460 
"17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE"       "17Q GAIN CNV" 
        TCGA-CG-4462         TCGA-CG-4465         TCGA-CG-4466 
"17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" 
        TCGA-CG-4469         TCGA-CG-4472         TCGA-CG-4474 
"17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" 
        TCGA-CG-4477         TCGA-CG-5716         TCGA-CG-5717 
"17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" 
        TCGA-CG-5718         TCGA-CG-5719         TCGA-CG-5720 
"17Q GAIN WILD-TYPE"       "17Q GAIN CNV" "17Q GAIN WILD-TYPE" 
        TCGA-CG-5721         TCGA-CG-5722         TCGA-CG-5723 
"17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" 
        TCGA-CG-5724         TCGA-CG-5725         TCGA-CG-5726 
      "17Q GAIN CNV" "17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" 
        TCGA-CG-5727         TCGA-CG-5728         TCGA-CG-5730 
"17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" 
        TCGA-CG-5732         TCGA-CG-5733         TCGA-CG-5734 
"17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" 
        TCGA-D7-5577         TCGA-D7-5578         TCGA-D7-5579 
"17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" 
        TCGA-D7-6518         TCGA-D7-6519         TCGA-D7-6520 
"17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" 
        TCGA-D7-6521         TCGA-D7-6522         TCGA-D7-6524 
"17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" 
        TCGA-D7-6525         TCGA-D7-6526         TCGA-D7-6527 
"17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" 
        TCGA-D7-6528         TCGA-D7-6815         TCGA-D7-6817 
"17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE"       "17Q GAIN CNV" 
        TCGA-D7-6818         TCGA-D7-6820         TCGA-D7-6822 
"17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" 
        TCGA-EQ-5647         TCGA-EQ-8122         TCGA-F1-6177 
      "17Q GAIN CNV" "17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" 
        TCGA-F1-6874         TCGA-F1-6875         TCGA-FP-7735 
"17Q GAIN WILD-TYPE"       "17Q GAIN CNV" "17Q GAIN WILD-TYPE" 
        TCGA-FP-7829         TCGA-FP-7916         TCGA-FP-7998 
      "17Q GAIN CNV" "17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" 
        TCGA-FP-8099         TCGA-FP-8209         TCGA-FP-8210 
"17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" 
        TCGA-FP-8631         TCGA-HJ-7597         TCGA-IN-7806 
"17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" 
        TCGA-IN-7808         TCGA-IP-7968 
"17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" 
        TCGA-B7-5816         TCGA-B7-5818         TCGA-BR-6452 
"17Q GAIN WILD-TYPE"       "17Q GAIN CNV" "17Q GAIN WILD-TYPE" 
        TCGA-BR-6455         TCGA-BR-6457         TCGA-BR-6458 
"17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" 
        TCGA-BR-6563         TCGA-BR-6564         TCGA-BR-6565 
"17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" 
        TCGA-BR-6566         TCGA-BR-6705         TCGA-BR-6706 
"17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" 
        TCGA-BR-6707         TCGA-BR-6709         TCGA-BR-6710 
"17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" 
        TCGA-BR-6801         TCGA-BR-6802         TCGA-BR-6803 
"17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" 
        TCGA-BR-6852         TCGA-BR-7196         TCGA-BR-7197 
"17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" 
        TCGA-BR-7703         TCGA-BR-7704         TCGA-BR-7707 
"17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" 
        TCGA-BR-7715         TCGA-BR-7716         TCGA-BR-7717 
"17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" 
        TCGA-BR-7722         TCGA-BR-7723         TCGA-BR-7851 
"17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" 
        TCGA-BR-7901         TCGA-BR-7957         TCGA-BR-7958 
"17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" 
        TCGA-BR-7959         TCGA-BR-8059         TCGA-BR-8060 
"17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" 
        TCGA-BR-8077         TCGA-BR-8078         TCGA-BR-8080 
"17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" 
        TCGA-BR-8081         TCGA-BR-8284         TCGA-BR-8285 
"17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" 
        TCGA-BR-8286         TCGA-BR-8289         TCGA-BR-8291 
"17Q GAIN WILD-TYPE"       "17Q GAIN CNV" "17Q GAIN WILD-TYPE" 
        TCGA-BR-8295         TCGA-BR-8296         TCGA-BR-8297 
"17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" 
        TCGA-BR-8592         TCGA-BR-A4IU         TCGA-BR-A4IV 
"17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" 
        TCGA-BR-A4IY         TCGA-BR-A4IZ         TCGA-BR-A4J1 
"17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" 
        TCGA-BR-A4J2         TCGA-BR-A4J4         TCGA-BR-A4J5 
"17Q GAIN WILD-TYPE"       "17Q GAIN CNV" "17Q GAIN WILD-TYPE" 
        TCGA-BR-A4J6         TCGA-BR-A4J8         TCGA-BR-A4J9 
"17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" 
        TCGA-BR-A4PF         TCGA-BR-A4QI         TCGA-BR-A4QL 
"17Q GAIN WILD-TYPE"       "17Q GAIN CNV" "17Q GAIN WILD-TYPE" 
        TCGA-CD-5798         TCGA-CD-5799         TCGA-CD-5800 
"17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" 
        TCGA-CD-5801         TCGA-CD-5802         TCGA-CD-5803 
"17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" 
        TCGA-CG-4300         TCGA-CG-4301         TCGA-CG-4304 
"17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" 
        TCGA-CG-4305         TCGA-CG-4306         TCGA-CG-4436 
"17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" 
        TCGA-CG-4437         TCGA-CG-4438         TCGA-CG-4440 
"17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" 
        TCGA-CG-4441         TCGA-CG-4443         TCGA-CG-4444 
"17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" 
        TCGA-CG-4449         TCGA-CG-4455         TCGA-CG-4460 
"17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE"       "17Q GAIN CNV" 
        TCGA-CG-4462         TCGA-CG-4465         TCGA-CG-4466 
"17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" 
        TCGA-CG-4469         TCGA-CG-4472         TCGA-CG-4474 
"17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" 
        TCGA-CG-4477         TCGA-CG-5716         TCGA-CG-5717 
"17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" 
        TCGA-CG-5718         TCGA-CG-5719         TCGA-CG-5720 
"17Q GAIN WILD-TYPE"       "17Q GAIN CNV" "17Q GAIN WILD-TYPE" 
        TCGA-CG-5721         TCGA-CG-5722         TCGA-CG-5723 
"17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" 
        TCGA-CG-5724         TCGA-CG-5725         TCGA-CG-5726 
      "17Q GAIN CNV" "17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" 
        TCGA-CG-5727         TCGA-CG-5728         TCGA-CG-5730 
"17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" 
        TCGA-CG-5732         TCGA-CG-5733         TCGA-CG-5734 
"17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" 
        TCGA-D7-5577         TCGA-D7-5578         TCGA-D7-5579 
"17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" 
        TCGA-D7-6518         TCGA-D7-6519         TCGA-D7-6520 
"17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" 
        TCGA-D7-6521         TCGA-D7-6522         TCGA-D7-6524 
"17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" 
        TCGA-D7-6525         TCGA-D7-6526         TCGA-D7-6527 
"17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" 
        TCGA-D7-6528         TCGA-D7-6815         TCGA-D7-6817 
"17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE"       "17Q GAIN CNV" 
        TCGA-D7-6818         TCGA-D7-6820         TCGA-D7-6822 
"17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" 
        TCGA-EQ-5647         TCGA-EQ-8122         TCGA-F1-6177 
      "17Q GAIN CNV" "17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" 
        TCGA-F1-6874         TCGA-F1-6875         TCGA-FP-7735 
"17Q GAIN WILD-TYPE"       "17Q GAIN CNV" "17Q GAIN WILD-TYPE" 
        TCGA-FP-7829         TCGA-FP-7916         TCGA-FP-7998 
      "17Q GAIN CNV" "17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" 
        TCGA-FP-8099         TCGA-FP-8209         TCGA-FP-8210 
"17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" 
        TCGA-FP-8631         TCGA-HJ-7597         TCGA-IN-7806 
"17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" 
        TCGA-IN-7808         TCGA-IP-7968 
"17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" 
[1] "hr=" "1.9"
D30V2, continuous
D30V3, binary
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  17Q GAIN CNV          4    8
  17Q GAIN WILD-TYPE   68  100
        clus
vv       17Q GAIN CNV 17Q GAIN WILD-TYPE
  FEMALE            4                 68
  MALE              8                100
                    vv
clus                 STOMACH  ADENOCARCINOMA  DIFFUSE TYPE
  17Q GAIN CNV                                           0
  17Q GAIN WILD-TYPE                                    10
                    vv
clus                 STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  17Q GAIN CNV                                                            2
  17Q GAIN WILD-TYPE                                                     14
                    vv
clus                 STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  17Q GAIN CNV                                                                       1
  17Q GAIN WILD-TYPE                                                                 7
                    vv
clus                 STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE
  17Q GAIN CNV                                                              0
  17Q GAIN WILD-TYPE                                                        3
                    vv
clus                 STOMACH ADENOCARCINOMA  SIGNET RING TYPE
  17Q GAIN CNV                                              0
  17Q GAIN WILD-TYPE                                        1
                    vv
clus                 STOMACH ADENOCARCINOMA - DIFFUSE TYPE
  17Q GAIN CNV                                           2
  17Q GAIN WILD-TYPE                                    14
                    vv
clus                 STOMACH ADENOCARCINOMA - NOT OTHERWISE SPECIFIED (NOS)
  17Q GAIN CNV                                                            3
  17Q GAIN WILD-TYPE                                                     70
                    vv
clus                 STOMACH INTESTINAL ADENOCARCINOMA - MUCINOUS TYPE
  17Q GAIN CNV                                                       1
  17Q GAIN WILD-TYPE                                                 6
                    vv
clus                 STOMACH INTESTINAL ADENOCARCINOMA - PAPILLARY TYPE
  17Q GAIN CNV                                                        0
  17Q GAIN WILD-TYPE                                                  3
                    vv
clus                 STOMACH INTESTINAL ADENOCARCINOMA - TUBULAR TYPE
  17Q GAIN CNV                                                      1
  17Q GAIN WILD-TYPE                                                9
                    vv
clus                 STOMACH INTESTINAL ADENOCARCINOMA - TYPE NOT OTHERWISE SPECIFIED (NOS)
  17Q GAIN CNV                                                                            2
  17Q GAIN WILD-TYPE                                                                     26
D30V4, multiclass
                    vv
clus                 T1 T2 T3 T4
  17Q GAIN CNV        0  3  3  3
  17Q GAIN WILD-TYPE  6 49 53 15
D30V5, multiclass
    clus
vv   17Q GAIN CNV 17Q GAIN WILD-TYPE
  T1            0                  6
  T2            3                 49
  T3            3                 53
  T4            3                 15
                    vv
clus                 N0 N1 N2 N3
  17Q GAIN CNV        4  2  0  3
  17Q GAIN WILD-TYPE 40 47 23 12
D30V6, multiclass
    clus
vv   17Q GAIN CNV 17Q GAIN WILD-TYPE
  N0            4                 40
  N1            2                 47
  N2            0                 23
  N3            3                 12
                    vv
clus                  M0  M1  MX
  17Q GAIN CNV         5   4   0
  17Q GAIN WILD-TYPE 113  12   8
D30V7, multiclass
    clus
vv   17Q GAIN CNV 17Q GAIN WILD-TYPE
  M0            5                113
  M1            4                 12
  MX            0                  8
                    vv
clus                  I II III IV
  17Q GAIN CNV        2  1   2  4
  17Q GAIN WILD-TYPE 22 36  37 22
D30V8, multiclass
     clus
vv    17Q GAIN CNV 17Q GAIN WILD-TYPE
  I              2                 22
  II             1                 36
  III            2                 37
  IV             4                 22
D30V9, binary
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  17Q GAIN CNV          0   12
  17Q GAIN WILD-TYPE    5  163
     clus
vv    17Q GAIN CNV 17Q GAIN WILD-TYPE
  NO             0                  5
  YES           12                163
                    vv
clus                  R0  R1  R2  RX
  17Q GAIN CNV         9   0   3   0
  17Q GAIN WILD-TYPE 116   7   9  25
D30V10, multiclass
    clus
vv   17Q GAIN CNV 17Q GAIN WILD-TYPE
  R0            9                116
  R1            0                  7
  R2            3                  9
  RX            0                 25
D30V11, continuous

Clustering(31) Variable = 18p gain
D31V1, survival
                    sevent
clus2                  0   1
  18P GAIN CNV        11   1
  18P GAIN WILD-TYPE 113  18
      18P GAIN CNV 18P GAIN WILD-TYPE 
                12                131 
      18P GAIN CNV 18P GAIN WILD-TYPE 
                 1                 18 
$`18P GAIN CNV`
TCGA-BR-7722 TCGA-BR-7901 TCGA-BR-8060 TCGA-BR-8295 TCGA-BR-A4J8 TCGA-BR-A4PF 
        0.16         0.95         1.32         1.55         0.23         0.72 
TCGA-CD-5799 TCGA-CG-4460 TCGA-CG-4474 TCGA-D7-6528 TCGA-D7-6817 TCGA-FP-8631 
        0.69        21.99         1.02         1.68         4.70         0.56 

$`18P GAIN WILD-TYPE`
TCGA-B7-5816 TCGA-B7-5818 TCGA-BR-6452 TCGA-BR-6455 TCGA-BR-6457 TCGA-BR-6458 
        5.62         0.10         0.95         1.41         1.35         1.35 
TCGA-BR-6563 TCGA-BR-6564 TCGA-BR-6565 TCGA-BR-6566 TCGA-BR-6705 TCGA-BR-6706 
        0.85         0.82         0.62         0.62         1.71         2.17 
TCGA-BR-6707 TCGA-BR-6709 TCGA-BR-6710 TCGA-BR-6801 TCGA-BR-6802 TCGA-BR-6803 
        0.99         1.22         0.66         1.12         0.76         0.66 
TCGA-BR-6852 TCGA-BR-7196 TCGA-BR-7197 TCGA-BR-7703 TCGA-BR-7704 TCGA-BR-7707 
        0.26         1.22         1.48         0.46         1.25         0.13 
TCGA-BR-7715 TCGA-BR-7716 TCGA-BR-7717 TCGA-BR-7723 TCGA-BR-7851 TCGA-BR-7957 
        1.05         0.82         0.69         4.54         0.99         0.69 
TCGA-BR-7958 TCGA-BR-7959 TCGA-BR-8059 TCGA-BR-8077 TCGA-BR-8078 TCGA-BR-8080 
        0.16         1.08         0.82         0.69         0.95         0.49 
TCGA-BR-8081 TCGA-BR-8284 TCGA-BR-8285 TCGA-BR-8286 TCGA-BR-8289 TCGA-BR-8291 
        0.46         0.72         0.26         0.43         0.26         1.18 
TCGA-BR-8296 TCGA-BR-8297 TCGA-BR-8592 TCGA-BR-A4IU TCGA-BR-A4IV TCGA-BR-A4IY 
        1.48         0.76         0.20         0.59         0.92         0.39 
TCGA-BR-A4IZ TCGA-BR-A4J1 TCGA-BR-A4J2 TCGA-BR-A4J4 TCGA-BR-A4J5 TCGA-BR-A4J6 
        0.79         0.72         0.79         0.53         0.43         0.13 
TCGA-BR-A4J9 TCGA-BR-A4QI TCGA-BR-A4QL TCGA-CD-5798 TCGA-CD-5800 TCGA-CD-5801 
        0.10         0.49         2.24         0.82         0.36         0.49 
TCGA-CD-5802 TCGA-CD-5803 TCGA-CG-4300 TCGA-CG-4301 TCGA-CG-4304 TCGA-CG-4305 
        0.30         0.07        20.02         3.02        27.02        15.95 
TCGA-CG-4306 TCGA-CG-4436 TCGA-CG-4437 TCGA-CG-4438 TCGA-CG-4440 TCGA-CG-4441 
        1.02        52.96         8.05        54.05         4.01        14.01 
TCGA-CG-4443 TCGA-CG-4444 TCGA-CG-4449 TCGA-CG-4455 TCGA-CG-4462 TCGA-CG-4465 
       29.98        47.05        19.07        12.03         1.02         8.98 
TCGA-CG-4466 TCGA-CG-4469 TCGA-CG-4472 TCGA-CG-4477 TCGA-CG-5716 TCGA-CG-5717 
       18.94         7.07        12.00         1.02         1.02         6.94 
TCGA-CG-5718 TCGA-CG-5719 TCGA-CG-5720 TCGA-CG-5721 TCGA-CG-5722 TCGA-CG-5723 
        1.02         1.02         0.99         5.98         0.95        70.06 
TCGA-CG-5724 TCGA-CG-5725 TCGA-CG-5726 TCGA-CG-5727 TCGA-CG-5728 TCGA-CG-5730 
       12.03        15.02        28.96        31.04        65.10         4.01 
TCGA-CG-5732 TCGA-CG-5733 TCGA-CG-5734 TCGA-D7-5577 TCGA-D7-5578 TCGA-D7-5579 
       55.04        21.07         7.99         8.65         3.58         4.54 
TCGA-D7-6518 TCGA-D7-6519 TCGA-D7-6520 TCGA-D7-6521 TCGA-D7-6522 TCGA-D7-6524 
        9.80        15.65         9.63         8.19         6.90         0.69 
TCGA-D7-6525 TCGA-D7-6526 TCGA-D7-6527 TCGA-D7-6815 TCGA-D7-6818 TCGA-D7-6820 
        5.95         6.61         4.14         3.65         4.04         2.93 
TCGA-D7-6822 TCGA-EQ-5647 TCGA-EQ-8122 TCGA-F1-6177 TCGA-F1-6874 TCGA-F1-6875 
        4.27         0.62         7.79         6.54         2.01        72.23 
TCGA-FP-7735 TCGA-FP-7829 TCGA-FP-7916 TCGA-FP-7998 TCGA-FP-8099 TCGA-FP-8209 
        0.39         0.20         3.02         3.58         1.02        59.05 
TCGA-FP-8210 TCGA-HJ-7597 TCGA-IN-7806 TCGA-IN-7808 TCGA-IP-7968 
        5.03        26.43         6.87         3.55         2.53 

      18P GAIN CNV 18P GAIN WILD-TYPE 
              0.16               0.07 
      18P GAIN CNV 18P GAIN WILD-TYPE 
             21.99              72.23 
      18P GAIN CNV 18P GAIN WILD-TYPE 
             0.985              1.350 
[1] "0.2 - 22.0 (1.0)" "0.1 - 72.2 (1.4)"
        TCGA-B7-5816         TCGA-B7-5818         TCGA-BR-6452 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-BR-6455         TCGA-BR-6457         TCGA-BR-6458 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-BR-6563         TCGA-BR-6564         TCGA-BR-6565 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-BR-6566         TCGA-BR-6705         TCGA-BR-6706 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-BR-6707         TCGA-BR-6709         TCGA-BR-6710 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-BR-6801         TCGA-BR-6802         TCGA-BR-6803 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-BR-6852         TCGA-BR-7196         TCGA-BR-7197 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-BR-7703         TCGA-BR-7704         TCGA-BR-7707 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-BR-7715         TCGA-BR-7716         TCGA-BR-7717 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-BR-7722         TCGA-BR-7723         TCGA-BR-7851 
      "18P GAIN CNV" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-BR-7901         TCGA-BR-7957         TCGA-BR-7958 
      "18P GAIN CNV" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-BR-7959         TCGA-BR-8059         TCGA-BR-8060 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE"       "18P GAIN CNV" 
        TCGA-BR-8077         TCGA-BR-8078         TCGA-BR-8080 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-BR-8081         TCGA-BR-8284         TCGA-BR-8285 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-BR-8286         TCGA-BR-8289         TCGA-BR-8291 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-BR-8295         TCGA-BR-8296         TCGA-BR-8297 
      "18P GAIN CNV" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-BR-8592         TCGA-BR-A4IU         TCGA-BR-A4IV 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-BR-A4IY         TCGA-BR-A4IZ         TCGA-BR-A4J1 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-BR-A4J2         TCGA-BR-A4J4         TCGA-BR-A4J5 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-BR-A4J6         TCGA-BR-A4J8         TCGA-BR-A4J9 
"18P GAIN WILD-TYPE"       "18P GAIN CNV" "18P GAIN WILD-TYPE" 
        TCGA-BR-A4PF         TCGA-BR-A4QI         TCGA-BR-A4QL 
      "18P GAIN CNV" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-CD-5798         TCGA-CD-5799         TCGA-CD-5800 
"18P GAIN WILD-TYPE"       "18P GAIN CNV" "18P GAIN WILD-TYPE" 
        TCGA-CD-5801         TCGA-CD-5802         TCGA-CD-5803 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-CG-4300         TCGA-CG-4301         TCGA-CG-4304 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-CG-4305         TCGA-CG-4306         TCGA-CG-4436 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-CG-4437         TCGA-CG-4438         TCGA-CG-4440 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-CG-4441         TCGA-CG-4443         TCGA-CG-4444 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-CG-4449         TCGA-CG-4455         TCGA-CG-4460 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE"       "18P GAIN CNV" 
        TCGA-CG-4462         TCGA-CG-4465         TCGA-CG-4466 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-CG-4469         TCGA-CG-4472         TCGA-CG-4474 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE"       "18P GAIN CNV" 
        TCGA-CG-4477         TCGA-CG-5716         TCGA-CG-5717 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-CG-5718         TCGA-CG-5719         TCGA-CG-5720 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-CG-5721         TCGA-CG-5722         TCGA-CG-5723 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-CG-5724         TCGA-CG-5725         TCGA-CG-5726 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-CG-5727         TCGA-CG-5728         TCGA-CG-5730 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-CG-5732         TCGA-CG-5733         TCGA-CG-5734 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-D7-5577         TCGA-D7-5578         TCGA-D7-5579 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-D7-6518         TCGA-D7-6519         TCGA-D7-6520 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-D7-6521         TCGA-D7-6522         TCGA-D7-6524 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-D7-6525         TCGA-D7-6526         TCGA-D7-6527 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-D7-6528         TCGA-D7-6815         TCGA-D7-6817 
      "18P GAIN CNV" "18P GAIN WILD-TYPE"       "18P GAIN CNV" 
        TCGA-D7-6818         TCGA-D7-6820         TCGA-D7-6822 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-EQ-5647         TCGA-EQ-8122         TCGA-F1-6177 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-F1-6874         TCGA-F1-6875         TCGA-FP-7735 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-FP-7829         TCGA-FP-7916         TCGA-FP-7998 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-FP-8099         TCGA-FP-8209         TCGA-FP-8210 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-FP-8631         TCGA-HJ-7597         TCGA-IN-7806 
      "18P GAIN CNV" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-IN-7808         TCGA-IP-7968 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-B7-5816         TCGA-B7-5818         TCGA-BR-6452 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-BR-6455         TCGA-BR-6457         TCGA-BR-6458 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-BR-6563         TCGA-BR-6564         TCGA-BR-6565 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-BR-6566         TCGA-BR-6705         TCGA-BR-6706 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-BR-6707         TCGA-BR-6709         TCGA-BR-6710 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-BR-6801         TCGA-BR-6802         TCGA-BR-6803 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-BR-6852         TCGA-BR-7196         TCGA-BR-7197 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-BR-7703         TCGA-BR-7704         TCGA-BR-7707 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-BR-7715         TCGA-BR-7716         TCGA-BR-7717 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-BR-7722         TCGA-BR-7723         TCGA-BR-7851 
      "18P GAIN CNV" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-BR-7901         TCGA-BR-7957         TCGA-BR-7958 
      "18P GAIN CNV" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-BR-7959         TCGA-BR-8059         TCGA-BR-8060 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE"       "18P GAIN CNV" 
        TCGA-BR-8077         TCGA-BR-8078         TCGA-BR-8080 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-BR-8081         TCGA-BR-8284         TCGA-BR-8285 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-BR-8286         TCGA-BR-8289         TCGA-BR-8291 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-BR-8295         TCGA-BR-8296         TCGA-BR-8297 
      "18P GAIN CNV" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-BR-8592         TCGA-BR-A4IU         TCGA-BR-A4IV 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-BR-A4IY         TCGA-BR-A4IZ         TCGA-BR-A4J1 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-BR-A4J2         TCGA-BR-A4J4         TCGA-BR-A4J5 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-BR-A4J6         TCGA-BR-A4J8         TCGA-BR-A4J9 
"18P GAIN WILD-TYPE"       "18P GAIN CNV" "18P GAIN WILD-TYPE" 
        TCGA-BR-A4PF         TCGA-BR-A4QI         TCGA-BR-A4QL 
      "18P GAIN CNV" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-CD-5798         TCGA-CD-5799         TCGA-CD-5800 
"18P GAIN WILD-TYPE"       "18P GAIN CNV" "18P GAIN WILD-TYPE" 
        TCGA-CD-5801         TCGA-CD-5802         TCGA-CD-5803 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-CG-4300         TCGA-CG-4301         TCGA-CG-4304 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-CG-4305         TCGA-CG-4306         TCGA-CG-4436 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-CG-4437         TCGA-CG-4438         TCGA-CG-4440 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-CG-4441         TCGA-CG-4443         TCGA-CG-4444 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-CG-4449         TCGA-CG-4455         TCGA-CG-4460 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE"       "18P GAIN CNV" 
        TCGA-CG-4462         TCGA-CG-4465         TCGA-CG-4466 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-CG-4469         TCGA-CG-4472         TCGA-CG-4474 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE"       "18P GAIN CNV" 
        TCGA-CG-4477         TCGA-CG-5716         TCGA-CG-5717 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-CG-5718         TCGA-CG-5719         TCGA-CG-5720 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-CG-5721         TCGA-CG-5722         TCGA-CG-5723 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-CG-5724         TCGA-CG-5725         TCGA-CG-5726 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-CG-5727         TCGA-CG-5728         TCGA-CG-5730 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-CG-5732         TCGA-CG-5733         TCGA-CG-5734 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-D7-5577         TCGA-D7-5578         TCGA-D7-5579 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-D7-6518         TCGA-D7-6519         TCGA-D7-6520 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-D7-6521         TCGA-D7-6522         TCGA-D7-6524 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-D7-6525         TCGA-D7-6526         TCGA-D7-6527 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-D7-6528         TCGA-D7-6815         TCGA-D7-6817 
      "18P GAIN CNV" "18P GAIN WILD-TYPE"       "18P GAIN CNV" 
        TCGA-D7-6818         TCGA-D7-6820         TCGA-D7-6822 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-EQ-5647         TCGA-EQ-8122         TCGA-F1-6177 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-F1-6874         TCGA-F1-6875         TCGA-FP-7735 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-FP-7829         TCGA-FP-7916         TCGA-FP-7998 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-FP-8099         TCGA-FP-8209         TCGA-FP-8210 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-FP-8631         TCGA-HJ-7597         TCGA-IN-7806 
      "18P GAIN CNV" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-IN-7808         TCGA-IP-7968 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-B7-5816         TCGA-B7-5818         TCGA-BR-6452 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-BR-6455         TCGA-BR-6457         TCGA-BR-6458 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-BR-6563         TCGA-BR-6564         TCGA-BR-6565 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-BR-6566         TCGA-BR-6705         TCGA-BR-6706 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-BR-6707         TCGA-BR-6709         TCGA-BR-6710 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-BR-6801         TCGA-BR-6802         TCGA-BR-6803 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-BR-6852         TCGA-BR-7196         TCGA-BR-7197 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-BR-7703         TCGA-BR-7704         TCGA-BR-7707 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-BR-7715         TCGA-BR-7716         TCGA-BR-7717 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-BR-7722         TCGA-BR-7723         TCGA-BR-7851 
      "18P GAIN CNV" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-BR-7901         TCGA-BR-7957         TCGA-BR-7958 
      "18P GAIN CNV" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-BR-7959         TCGA-BR-8059         TCGA-BR-8060 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE"       "18P GAIN CNV" 
        TCGA-BR-8077         TCGA-BR-8078         TCGA-BR-8080 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-BR-8081         TCGA-BR-8284         TCGA-BR-8285 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-BR-8286         TCGA-BR-8289         TCGA-BR-8291 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-BR-8295         TCGA-BR-8296         TCGA-BR-8297 
      "18P GAIN CNV" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-BR-8592         TCGA-BR-A4IU         TCGA-BR-A4IV 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-BR-A4IY         TCGA-BR-A4IZ         TCGA-BR-A4J1 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-BR-A4J2         TCGA-BR-A4J4         TCGA-BR-A4J5 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-BR-A4J6         TCGA-BR-A4J8         TCGA-BR-A4J9 
"18P GAIN WILD-TYPE"       "18P GAIN CNV" "18P GAIN WILD-TYPE" 
        TCGA-BR-A4PF         TCGA-BR-A4QI         TCGA-BR-A4QL 
      "18P GAIN CNV" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-CD-5798         TCGA-CD-5799         TCGA-CD-5800 
"18P GAIN WILD-TYPE"       "18P GAIN CNV" "18P GAIN WILD-TYPE" 
        TCGA-CD-5801         TCGA-CD-5802         TCGA-CD-5803 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-CG-4300         TCGA-CG-4301         TCGA-CG-4304 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-CG-4305         TCGA-CG-4306         TCGA-CG-4436 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-CG-4437         TCGA-CG-4438         TCGA-CG-4440 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-CG-4441         TCGA-CG-4443         TCGA-CG-4444 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-CG-4449         TCGA-CG-4455         TCGA-CG-4460 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE"       "18P GAIN CNV" 
        TCGA-CG-4462         TCGA-CG-4465         TCGA-CG-4466 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-CG-4469         TCGA-CG-4472         TCGA-CG-4474 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE"       "18P GAIN CNV" 
        TCGA-CG-4477         TCGA-CG-5716         TCGA-CG-5717 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-CG-5718         TCGA-CG-5719         TCGA-CG-5720 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-CG-5721         TCGA-CG-5722         TCGA-CG-5723 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-CG-5724         TCGA-CG-5725         TCGA-CG-5726 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-CG-5727         TCGA-CG-5728         TCGA-CG-5730 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-CG-5732         TCGA-CG-5733         TCGA-CG-5734 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-D7-5577         TCGA-D7-5578         TCGA-D7-5579 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-D7-6518         TCGA-D7-6519         TCGA-D7-6520 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-D7-6521         TCGA-D7-6522         TCGA-D7-6524 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-D7-6525         TCGA-D7-6526         TCGA-D7-6527 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-D7-6528         TCGA-D7-6815         TCGA-D7-6817 
      "18P GAIN CNV" "18P GAIN WILD-TYPE"       "18P GAIN CNV" 
        TCGA-D7-6818         TCGA-D7-6820         TCGA-D7-6822 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-EQ-5647         TCGA-EQ-8122         TCGA-F1-6177 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-F1-6874         TCGA-F1-6875         TCGA-FP-7735 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-FP-7829         TCGA-FP-7916         TCGA-FP-7998 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-FP-8099         TCGA-FP-8209         TCGA-FP-8210 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-FP-8631         TCGA-HJ-7597         TCGA-IN-7806 
      "18P GAIN CNV" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-IN-7808         TCGA-IP-7968 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
[1] "hr=" "1.4"
D31V2, continuous
D31V3, binary
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  18P GAIN CNV          8   10
  18P GAIN WILD-TYPE   64   98
        clus
vv       18P GAIN CNV 18P GAIN WILD-TYPE
  FEMALE            8                 64
  MALE             10                 98
                    vv
clus                 STOMACH  ADENOCARCINOMA  DIFFUSE TYPE
  18P GAIN CNV                                           0
  18P GAIN WILD-TYPE                                    10
                    vv
clus                 STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  18P GAIN CNV                                                            4
  18P GAIN WILD-TYPE                                                     12
                    vv
clus                 STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  18P GAIN CNV                                                                       1
  18P GAIN WILD-TYPE                                                                 7
                    vv
clus                 STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE
  18P GAIN CNV                                                              0
  18P GAIN WILD-TYPE                                                        3
                    vv
clus                 STOMACH ADENOCARCINOMA  SIGNET RING TYPE
  18P GAIN CNV                                              0
  18P GAIN WILD-TYPE                                        1
                    vv
clus                 STOMACH ADENOCARCINOMA - DIFFUSE TYPE
  18P GAIN CNV                                           1
  18P GAIN WILD-TYPE                                    15
                    vv
clus                 STOMACH ADENOCARCINOMA - NOT OTHERWISE SPECIFIED (NOS)
  18P GAIN CNV                                                            6
  18P GAIN WILD-TYPE                                                     67
                    vv
clus                 STOMACH INTESTINAL ADENOCARCINOMA - MUCINOUS TYPE
  18P GAIN CNV                                                       1
  18P GAIN WILD-TYPE                                                 6
                    vv
clus                 STOMACH INTESTINAL ADENOCARCINOMA - PAPILLARY TYPE
  18P GAIN CNV                                                        0
  18P GAIN WILD-TYPE                                                  3
                    vv
clus                 STOMACH INTESTINAL ADENOCARCINOMA - TUBULAR TYPE
  18P GAIN CNV                                                      2
  18P GAIN WILD-TYPE                                                8
                    vv
clus                 STOMACH INTESTINAL ADENOCARCINOMA - TYPE NOT OTHERWISE SPECIFIED (NOS)
  18P GAIN CNV                                                                            2
  18P GAIN WILD-TYPE                                                                     26
D31V4, multiclass
                    vv
clus                 T1 T2 T3 T4
  18P GAIN CNV        0  4  5  2
  18P GAIN WILD-TYPE  6 48 51 16
D31V5, multiclass
    clus
vv   18P GAIN CNV 18P GAIN WILD-TYPE
  T1            0                  6
  T2            4                 48
  T3            5                 51
  T4            2                 16
                    vv
clus                 N0 N1 N2 N3
  18P GAIN CNV        1  8  1  2
  18P GAIN WILD-TYPE 43 41 22 13
D31V6, multiclass
    clus
vv   18P GAIN CNV 18P GAIN WILD-TYPE
  N0            1                 43
  N1            8                 41
  N2            1                 22
  N3            2                 13
                    vv
clus                  M0  M1  MX
  18P GAIN CNV        10   2   1
  18P GAIN WILD-TYPE 108  14   7
D31V7, multiclass
    clus
vv   18P GAIN CNV 18P GAIN WILD-TYPE
  M0           10                108
  M1            2                 14
  MX            1                  7
                    vv
clus                  I II III IV
  18P GAIN CNV        1  2   5  3
  18P GAIN WILD-TYPE 23 35  34 23
D31V8, multiclass
     clus
vv    18P GAIN CNV 18P GAIN WILD-TYPE
  I              1                 23
  II             2                 35
  III            5                 34
  IV             3                 23
D31V9, binary
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  18P GAIN CNV          1   17
  18P GAIN WILD-TYPE    4  158
     clus
vv    18P GAIN CNV 18P GAIN WILD-TYPE
  NO             1                  4
  YES           17                158
                    vv
clus                  R0  R1  R2  RX
  18P GAIN CNV        11   1   2   3
  18P GAIN WILD-TYPE 114   6  10  22
D31V10, multiclass
    clus
vv   18P GAIN CNV 18P GAIN WILD-TYPE
  R0           11                114
  R1            1                  6
  R2            2                 10
  RX            3                 22
D31V11, continuous

Clustering(32) Variable = 18q gain
D32V1, survival
                    sevent
clus2                  0   1
  18Q GAIN CNV         7   1
  18Q GAIN WILD-TYPE 117  18
      18Q GAIN CNV 18Q GAIN WILD-TYPE 
                 8                135 
      18Q GAIN CNV 18Q GAIN WILD-TYPE 
                 1                 18 
$`18Q GAIN CNV`
TCGA-BR-8295 TCGA-BR-A4PF TCGA-CD-5799 TCGA-CG-4460 TCGA-CG-4474 TCGA-D7-6528 
        1.55         0.72         0.69        21.99         1.02         1.68 
TCGA-D7-6817 TCGA-FP-8631 
        4.70         0.56 

$`18Q GAIN WILD-TYPE`
TCGA-B7-5816 TCGA-B7-5818 TCGA-BR-6452 TCGA-BR-6455 TCGA-BR-6457 TCGA-BR-6458 
        5.62         0.10         0.95         1.41         1.35         1.35 
TCGA-BR-6563 TCGA-BR-6564 TCGA-BR-6565 TCGA-BR-6566 TCGA-BR-6705 TCGA-BR-6706 
        0.85         0.82         0.62         0.62         1.71         2.17 
TCGA-BR-6707 TCGA-BR-6709 TCGA-BR-6710 TCGA-BR-6801 TCGA-BR-6802 TCGA-BR-6803 
        0.99         1.22         0.66         1.12         0.76         0.66 
TCGA-BR-6852 TCGA-BR-7196 TCGA-BR-7197 TCGA-BR-7703 TCGA-BR-7704 TCGA-BR-7707 
        0.26         1.22         1.48         0.46         1.25         0.13 
TCGA-BR-7715 TCGA-BR-7716 TCGA-BR-7717 TCGA-BR-7722 TCGA-BR-7723 TCGA-BR-7851 
        1.05         0.82         0.69         0.16         4.54         0.99 
TCGA-BR-7901 TCGA-BR-7957 TCGA-BR-7958 TCGA-BR-7959 TCGA-BR-8059 TCGA-BR-8060 
        0.95         0.69         0.16         1.08         0.82         1.32 
TCGA-BR-8077 TCGA-BR-8078 TCGA-BR-8080 TCGA-BR-8081 TCGA-BR-8284 TCGA-BR-8285 
        0.69         0.95         0.49         0.46         0.72         0.26 
TCGA-BR-8286 TCGA-BR-8289 TCGA-BR-8291 TCGA-BR-8296 TCGA-BR-8297 TCGA-BR-8592 
        0.43         0.26         1.18         1.48         0.76         0.20 
TCGA-BR-A4IU TCGA-BR-A4IV TCGA-BR-A4IY TCGA-BR-A4IZ TCGA-BR-A4J1 TCGA-BR-A4J2 
        0.59         0.92         0.39         0.79         0.72         0.79 
TCGA-BR-A4J4 TCGA-BR-A4J5 TCGA-BR-A4J6 TCGA-BR-A4J8 TCGA-BR-A4J9 TCGA-BR-A4QI 
        0.53         0.43         0.13         0.23         0.10         0.49 
TCGA-BR-A4QL TCGA-CD-5798 TCGA-CD-5800 TCGA-CD-5801 TCGA-CD-5802 TCGA-CD-5803 
        2.24         0.82         0.36         0.49         0.30         0.07 
TCGA-CG-4300 TCGA-CG-4301 TCGA-CG-4304 TCGA-CG-4305 TCGA-CG-4306 TCGA-CG-4436 
       20.02         3.02        27.02        15.95         1.02        52.96 
TCGA-CG-4437 TCGA-CG-4438 TCGA-CG-4440 TCGA-CG-4441 TCGA-CG-4443 TCGA-CG-4444 
        8.05        54.05         4.01        14.01        29.98        47.05 
TCGA-CG-4449 TCGA-CG-4455 TCGA-CG-4462 TCGA-CG-4465 TCGA-CG-4466 TCGA-CG-4469 
       19.07        12.03         1.02         8.98        18.94         7.07 
TCGA-CG-4472 TCGA-CG-4477 TCGA-CG-5716 TCGA-CG-5717 TCGA-CG-5718 TCGA-CG-5719 
       12.00         1.02         1.02         6.94         1.02         1.02 
TCGA-CG-5720 TCGA-CG-5721 TCGA-CG-5722 TCGA-CG-5723 TCGA-CG-5724 TCGA-CG-5725 
        0.99         5.98         0.95        70.06        12.03        15.02 
TCGA-CG-5726 TCGA-CG-5727 TCGA-CG-5728 TCGA-CG-5730 TCGA-CG-5732 TCGA-CG-5733 
       28.96        31.04        65.10         4.01        55.04        21.07 
TCGA-CG-5734 TCGA-D7-5577 TCGA-D7-5578 TCGA-D7-5579 TCGA-D7-6518 TCGA-D7-6519 
        7.99         8.65         3.58         4.54         9.80        15.65 
TCGA-D7-6520 TCGA-D7-6521 TCGA-D7-6522 TCGA-D7-6524 TCGA-D7-6525 TCGA-D7-6526 
        9.63         8.19         6.90         0.69         5.95         6.61 
TCGA-D7-6527 TCGA-D7-6815 TCGA-D7-6818 TCGA-D7-6820 TCGA-D7-6822 TCGA-EQ-5647 
        4.14         3.65         4.04         2.93         4.27         0.62 
TCGA-EQ-8122 TCGA-F1-6177 TCGA-F1-6874 TCGA-F1-6875 TCGA-FP-7735 TCGA-FP-7829 
        7.79         6.54         2.01        72.23         0.39         0.20 
TCGA-FP-7916 TCGA-FP-7998 TCGA-FP-8099 TCGA-FP-8209 TCGA-FP-8210 TCGA-HJ-7597 
        3.02         3.58         1.02        59.05         5.03        26.43 
TCGA-IN-7806 TCGA-IN-7808 TCGA-IP-7968 
        6.87         3.55         2.53 

      18Q GAIN CNV 18Q GAIN WILD-TYPE 
              0.56               0.07 
      18Q GAIN CNV 18Q GAIN WILD-TYPE 
             21.99              72.23 
      18Q GAIN CNV 18Q GAIN WILD-TYPE 
             1.285              1.250 
[1] "0.6 - 22.0 (1.3)" "0.1 - 72.2 (1.2)"
        TCGA-B7-5816         TCGA-B7-5818         TCGA-BR-6452 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-BR-6455         TCGA-BR-6457         TCGA-BR-6458 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-BR-6563         TCGA-BR-6564         TCGA-BR-6565 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-BR-6566         TCGA-BR-6705         TCGA-BR-6706 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-BR-6707         TCGA-BR-6709         TCGA-BR-6710 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-BR-6801         TCGA-BR-6802         TCGA-BR-6803 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-BR-6852         TCGA-BR-7196         TCGA-BR-7197 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-BR-7703         TCGA-BR-7704         TCGA-BR-7707 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-BR-7715         TCGA-BR-7716         TCGA-BR-7717 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-BR-7722         TCGA-BR-7723         TCGA-BR-7851 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-BR-7901         TCGA-BR-7957         TCGA-BR-7958 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-BR-7959         TCGA-BR-8059         TCGA-BR-8060 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-BR-8077         TCGA-BR-8078         TCGA-BR-8080 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-BR-8081         TCGA-BR-8284         TCGA-BR-8285 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-BR-8286         TCGA-BR-8289         TCGA-BR-8291 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-BR-8295         TCGA-BR-8296         TCGA-BR-8297 
      "18Q GAIN CNV" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-BR-8592         TCGA-BR-A4IU         TCGA-BR-A4IV 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-BR-A4IY         TCGA-BR-A4IZ         TCGA-BR-A4J1 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-BR-A4J2         TCGA-BR-A4J4         TCGA-BR-A4J5 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-BR-A4J6         TCGA-BR-A4J8         TCGA-BR-A4J9 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-BR-A4PF         TCGA-BR-A4QI         TCGA-BR-A4QL 
      "18Q GAIN CNV" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-CD-5798         TCGA-CD-5799         TCGA-CD-5800 
"18Q GAIN WILD-TYPE"       "18Q GAIN CNV" "18Q GAIN WILD-TYPE" 
        TCGA-CD-5801         TCGA-CD-5802         TCGA-CD-5803 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-CG-4300         TCGA-CG-4301         TCGA-CG-4304 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-CG-4305         TCGA-CG-4306         TCGA-CG-4436 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-CG-4437         TCGA-CG-4438         TCGA-CG-4440 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-CG-4441         TCGA-CG-4443         TCGA-CG-4444 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-CG-4449         TCGA-CG-4455         TCGA-CG-4460 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE"       "18Q GAIN CNV" 
        TCGA-CG-4462         TCGA-CG-4465         TCGA-CG-4466 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-CG-4469         TCGA-CG-4472         TCGA-CG-4474 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE"       "18Q GAIN CNV" 
        TCGA-CG-4477         TCGA-CG-5716         TCGA-CG-5717 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-CG-5718         TCGA-CG-5719         TCGA-CG-5720 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-CG-5721         TCGA-CG-5722         TCGA-CG-5723 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-CG-5724         TCGA-CG-5725         TCGA-CG-5726 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-CG-5727         TCGA-CG-5728         TCGA-CG-5730 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-CG-5732         TCGA-CG-5733         TCGA-CG-5734 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-D7-5577         TCGA-D7-5578         TCGA-D7-5579 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-D7-6518         TCGA-D7-6519         TCGA-D7-6520 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-D7-6521         TCGA-D7-6522         TCGA-D7-6524 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-D7-6525         TCGA-D7-6526         TCGA-D7-6527 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-D7-6528         TCGA-D7-6815         TCGA-D7-6817 
      "18Q GAIN CNV" "18Q GAIN WILD-TYPE"       "18Q GAIN CNV" 
        TCGA-D7-6818         TCGA-D7-6820         TCGA-D7-6822 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-EQ-5647         TCGA-EQ-8122         TCGA-F1-6177 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-F1-6874         TCGA-F1-6875         TCGA-FP-7735 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-FP-7829         TCGA-FP-7916         TCGA-FP-7998 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-FP-8099         TCGA-FP-8209         TCGA-FP-8210 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-FP-8631         TCGA-HJ-7597         TCGA-IN-7806 
      "18Q GAIN CNV" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-IN-7808         TCGA-IP-7968 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-B7-5816         TCGA-B7-5818         TCGA-BR-6452 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-BR-6455         TCGA-BR-6457         TCGA-BR-6458 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-BR-6563         TCGA-BR-6564         TCGA-BR-6565 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-BR-6566         TCGA-BR-6705         TCGA-BR-6706 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-BR-6707         TCGA-BR-6709         TCGA-BR-6710 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-BR-6801         TCGA-BR-6802         TCGA-BR-6803 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-BR-6852         TCGA-BR-7196         TCGA-BR-7197 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-BR-7703         TCGA-BR-7704         TCGA-BR-7707 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-BR-7715         TCGA-BR-7716         TCGA-BR-7717 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-BR-7722         TCGA-BR-7723         TCGA-BR-7851 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-BR-7901         TCGA-BR-7957         TCGA-BR-7958 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-BR-7959         TCGA-BR-8059         TCGA-BR-8060 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-BR-8077         TCGA-BR-8078         TCGA-BR-8080 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-BR-8081         TCGA-BR-8284         TCGA-BR-8285 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-BR-8286         TCGA-BR-8289         TCGA-BR-8291 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-BR-8295         TCGA-BR-8296         TCGA-BR-8297 
      "18Q GAIN CNV" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-BR-8592         TCGA-BR-A4IU         TCGA-BR-A4IV 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-BR-A4IY         TCGA-BR-A4IZ         TCGA-BR-A4J1 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-BR-A4J2         TCGA-BR-A4J4         TCGA-BR-A4J5 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-BR-A4J6         TCGA-BR-A4J8         TCGA-BR-A4J9 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-BR-A4PF         TCGA-BR-A4QI         TCGA-BR-A4QL 
      "18Q GAIN CNV" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-CD-5798         TCGA-CD-5799         TCGA-CD-5800 
"18Q GAIN WILD-TYPE"       "18Q GAIN CNV" "18Q GAIN WILD-TYPE" 
        TCGA-CD-5801         TCGA-CD-5802         TCGA-CD-5803 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-CG-4300         TCGA-CG-4301         TCGA-CG-4304 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-CG-4305         TCGA-CG-4306         TCGA-CG-4436 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-CG-4437         TCGA-CG-4438         TCGA-CG-4440 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-CG-4441         TCGA-CG-4443         TCGA-CG-4444 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-CG-4449         TCGA-CG-4455         TCGA-CG-4460 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE"       "18Q GAIN CNV" 
        TCGA-CG-4462         TCGA-CG-4465         TCGA-CG-4466 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-CG-4469         TCGA-CG-4472         TCGA-CG-4474 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE"       "18Q GAIN CNV" 
        TCGA-CG-4477         TCGA-CG-5716         TCGA-CG-5717 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-CG-5718         TCGA-CG-5719         TCGA-CG-5720 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-CG-5721         TCGA-CG-5722         TCGA-CG-5723 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-CG-5724         TCGA-CG-5725         TCGA-CG-5726 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-CG-5727         TCGA-CG-5728         TCGA-CG-5730 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-CG-5732         TCGA-CG-5733         TCGA-CG-5734 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-D7-5577         TCGA-D7-5578         TCGA-D7-5579 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-D7-6518         TCGA-D7-6519         TCGA-D7-6520 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-D7-6521         TCGA-D7-6522         TCGA-D7-6524 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-D7-6525         TCGA-D7-6526         TCGA-D7-6527 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-D7-6528         TCGA-D7-6815         TCGA-D7-6817 
      "18Q GAIN CNV" "18Q GAIN WILD-TYPE"       "18Q GAIN CNV" 
        TCGA-D7-6818         TCGA-D7-6820         TCGA-D7-6822 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-EQ-5647         TCGA-EQ-8122         TCGA-F1-6177 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-F1-6874         TCGA-F1-6875         TCGA-FP-7735 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-FP-7829         TCGA-FP-7916         TCGA-FP-7998 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-FP-8099         TCGA-FP-8209         TCGA-FP-8210 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-FP-8631         TCGA-HJ-7597         TCGA-IN-7806 
      "18Q GAIN CNV" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-IN-7808         TCGA-IP-7968 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-B7-5816         TCGA-B7-5818         TCGA-BR-6452 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-BR-6455         TCGA-BR-6457         TCGA-BR-6458 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-BR-6563         TCGA-BR-6564         TCGA-BR-6565 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-BR-6566         TCGA-BR-6705         TCGA-BR-6706 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-BR-6707         TCGA-BR-6709         TCGA-BR-6710 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-BR-6801         TCGA-BR-6802         TCGA-BR-6803 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-BR-6852         TCGA-BR-7196         TCGA-BR-7197 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-BR-7703         TCGA-BR-7704         TCGA-BR-7707 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-BR-7715         TCGA-BR-7716         TCGA-BR-7717 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-BR-7722         TCGA-BR-7723         TCGA-BR-7851 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-BR-7901         TCGA-BR-7957         TCGA-BR-7958 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-BR-7959         TCGA-BR-8059         TCGA-BR-8060 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-BR-8077         TCGA-BR-8078         TCGA-BR-8080 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-BR-8081         TCGA-BR-8284         TCGA-BR-8285 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-BR-8286         TCGA-BR-8289         TCGA-BR-8291 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-BR-8295         TCGA-BR-8296         TCGA-BR-8297 
      "18Q GAIN CNV" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-BR-8592         TCGA-BR-A4IU         TCGA-BR-A4IV 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-BR-A4IY         TCGA-BR-A4IZ         TCGA-BR-A4J1 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-BR-A4J2         TCGA-BR-A4J4         TCGA-BR-A4J5 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-BR-A4J6         TCGA-BR-A4J8         TCGA-BR-A4J9 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-BR-A4PF         TCGA-BR-A4QI         TCGA-BR-A4QL 
      "18Q GAIN CNV" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-CD-5798         TCGA-CD-5799         TCGA-CD-5800 
"18Q GAIN WILD-TYPE"       "18Q GAIN CNV" "18Q GAIN WILD-TYPE" 
        TCGA-CD-5801         TCGA-CD-5802         TCGA-CD-5803 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-CG-4300         TCGA-CG-4301         TCGA-CG-4304 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-CG-4305         TCGA-CG-4306         TCGA-CG-4436 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-CG-4437         TCGA-CG-4438         TCGA-CG-4440 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-CG-4441         TCGA-CG-4443         TCGA-CG-4444 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-CG-4449         TCGA-CG-4455         TCGA-CG-4460 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE"       "18Q GAIN CNV" 
        TCGA-CG-4462         TCGA-CG-4465         TCGA-CG-4466 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-CG-4469         TCGA-CG-4472         TCGA-CG-4474 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE"       "18Q GAIN CNV" 
        TCGA-CG-4477         TCGA-CG-5716         TCGA-CG-5717 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-CG-5718         TCGA-CG-5719         TCGA-CG-5720 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-CG-5721         TCGA-CG-5722         TCGA-CG-5723 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-CG-5724         TCGA-CG-5725         TCGA-CG-5726 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-CG-5727         TCGA-CG-5728         TCGA-CG-5730 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-CG-5732         TCGA-CG-5733         TCGA-CG-5734 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-D7-5577         TCGA-D7-5578         TCGA-D7-5579 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-D7-6518         TCGA-D7-6519         TCGA-D7-6520 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-D7-6521         TCGA-D7-6522         TCGA-D7-6524 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-D7-6525         TCGA-D7-6526         TCGA-D7-6527 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-D7-6528         TCGA-D7-6815         TCGA-D7-6817 
      "18Q GAIN CNV" "18Q GAIN WILD-TYPE"       "18Q GAIN CNV" 
        TCGA-D7-6818         TCGA-D7-6820         TCGA-D7-6822 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-EQ-5647         TCGA-EQ-8122         TCGA-F1-6177 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-F1-6874         TCGA-F1-6875         TCGA-FP-7735 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-FP-7829         TCGA-FP-7916         TCGA-FP-7998 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-FP-8099         TCGA-FP-8209         TCGA-FP-8210 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-FP-8631         TCGA-HJ-7597         TCGA-IN-7806 
      "18Q GAIN CNV" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-IN-7808         TCGA-IP-7968 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
[1] "hr=" "1.5"
D32V2, continuous
D32V3, binary
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  18Q GAIN CNV          5    5
  18Q GAIN WILD-TYPE   67  103
        clus
vv       18Q GAIN CNV 18Q GAIN WILD-TYPE
  FEMALE            5                 67
  MALE              5                103
                    vv
clus                 STOMACH  ADENOCARCINOMA  DIFFUSE TYPE
  18Q GAIN CNV                                           0
  18Q GAIN WILD-TYPE                                    10
                    vv
clus                 STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  18Q GAIN CNV                                                            2
  18Q GAIN WILD-TYPE                                                     14
                    vv
clus                 STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  18Q GAIN CNV                                                                       1
  18Q GAIN WILD-TYPE                                                                 7
                    vv
clus                 STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE
  18Q GAIN CNV                                                              0
  18Q GAIN WILD-TYPE                                                        3
                    vv
clus                 STOMACH ADENOCARCINOMA  SIGNET RING TYPE
  18Q GAIN CNV                                              0
  18Q GAIN WILD-TYPE                                        1
                    vv
clus                 STOMACH ADENOCARCINOMA - DIFFUSE TYPE
  18Q GAIN CNV                                           1
  18Q GAIN WILD-TYPE                                    15
                    vv
clus                 STOMACH ADENOCARCINOMA - NOT OTHERWISE SPECIFIED (NOS)
  18Q GAIN CNV                                                            2
  18Q GAIN WILD-TYPE                                                     71
                    vv
clus                 STOMACH INTESTINAL ADENOCARCINOMA - MUCINOUS TYPE
  18Q GAIN CNV                                                       0
  18Q GAIN WILD-TYPE                                                 7
                    vv
clus                 STOMACH INTESTINAL ADENOCARCINOMA - PAPILLARY TYPE
  18Q GAIN CNV                                                        0
  18Q GAIN WILD-TYPE                                                  3
                    vv
clus                 STOMACH INTESTINAL ADENOCARCINOMA - TUBULAR TYPE
  18Q GAIN CNV                                                      2
  18Q GAIN WILD-TYPE                                                8
                    vv
clus                 STOMACH INTESTINAL ADENOCARCINOMA - TYPE NOT OTHERWISE SPECIFIED (NOS)
  18Q GAIN CNV                                                                            2
  18Q GAIN WILD-TYPE                                                                     26
D32V4, multiclass
                    vv
clus                 T1 T2 T3 T4
  18Q GAIN CNV        0  3  1  2
  18Q GAIN WILD-TYPE  6 49 55 16
D32V5, multiclass
    clus
vv   18Q GAIN CNV 18Q GAIN WILD-TYPE
  T1            0                  6
  T2            3                 49
  T3            1                 55
  T4            2                 16
                    vv
clus                 N0 N1 N2 N3
  18Q GAIN CNV        1  3  1  1
  18Q GAIN WILD-TYPE 43 46 22 14
D32V6, multiclass
    clus
vv   18Q GAIN CNV 18Q GAIN WILD-TYPE
  N0            1                 43
  N1            3                 46
  N2            1                 22
  N3            1                 14
                    vv
clus                  M0  M1  MX
  18Q GAIN CNV         4   2   1
  18Q GAIN WILD-TYPE 114  14   7
D32V7, multiclass
    clus
vv   18Q GAIN CNV 18Q GAIN WILD-TYPE
  M0            4                114
  M1            2                 14
  MX            1                  7
                    vv
clus                  I II III IV
  18Q GAIN CNV        1  1   2  2
  18Q GAIN WILD-TYPE 23 36  37 24
D32V8, multiclass
     clus
vv    18Q GAIN CNV 18Q GAIN WILD-TYPE
  I              1                 23
  II             1                 36
  III            2                 37
  IV             2                 24
D32V9, binary
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  18Q GAIN CNV          0   10
  18Q GAIN WILD-TYPE    5  165
     clus
vv    18Q GAIN CNV 18Q GAIN WILD-TYPE
  NO             0                  5
  YES           10                165
                    vv
clus                  R0  R1  R2  RX
  18Q GAIN CNV         5   0   2   2
  18Q GAIN WILD-TYPE 120   7  10  23
D32V10, multiclass
    clus
vv   18Q GAIN CNV 18Q GAIN WILD-TYPE
  R0            5                120
  R1            0                  7
  R2            2                 10
  RX            2                 23
D32V11, continuous

Clustering(33) Variable = 19p gain
D33V1, survival
                    sevent
clus2                  0   1
  19P GAIN CNV         6   1
  19P GAIN WILD-TYPE 118  18
      19P GAIN CNV 19P GAIN WILD-TYPE 
                 7                136 
      19P GAIN CNV 19P GAIN WILD-TYPE 
                 1                 18 
$`19P GAIN CNV`
TCGA-CG-4460 TCGA-CG-4474 TCGA-CG-5722 TCGA-CG-5730 TCGA-D7-5577 TCGA-D7-6518 
       21.99         1.02         0.95         4.01         8.65         9.80 
TCGA-D7-6521 
        8.19 

$`19P GAIN WILD-TYPE`
TCGA-B7-5816 TCGA-B7-5818 TCGA-BR-6452 TCGA-BR-6455 TCGA-BR-6457 TCGA-BR-6458 
        5.62         0.10         0.95         1.41         1.35         1.35 
TCGA-BR-6563 TCGA-BR-6564 TCGA-BR-6565 TCGA-BR-6566 TCGA-BR-6705 TCGA-BR-6706 
        0.85         0.82         0.62         0.62         1.71         2.17 
TCGA-BR-6707 TCGA-BR-6709 TCGA-BR-6710 TCGA-BR-6801 TCGA-BR-6802 TCGA-BR-6803 
        0.99         1.22         0.66         1.12         0.76         0.66 
TCGA-BR-6852 TCGA-BR-7196 TCGA-BR-7197 TCGA-BR-7703 TCGA-BR-7704 TCGA-BR-7707 
        0.26         1.22         1.48         0.46         1.25         0.13 
TCGA-BR-7715 TCGA-BR-7716 TCGA-BR-7717 TCGA-BR-7722 TCGA-BR-7723 TCGA-BR-7851 
        1.05         0.82         0.69         0.16         4.54         0.99 
TCGA-BR-7901 TCGA-BR-7957 TCGA-BR-7958 TCGA-BR-7959 TCGA-BR-8059 TCGA-BR-8060 
        0.95         0.69         0.16         1.08         0.82         1.32 
TCGA-BR-8077 TCGA-BR-8078 TCGA-BR-8080 TCGA-BR-8081 TCGA-BR-8284 TCGA-BR-8285 
        0.69         0.95         0.49         0.46         0.72         0.26 
TCGA-BR-8286 TCGA-BR-8289 TCGA-BR-8291 TCGA-BR-8295 TCGA-BR-8296 TCGA-BR-8297 
        0.43         0.26         1.18         1.55         1.48         0.76 
TCGA-BR-8592 TCGA-BR-A4IU TCGA-BR-A4IV TCGA-BR-A4IY TCGA-BR-A4IZ TCGA-BR-A4J1 
        0.20         0.59         0.92         0.39         0.79         0.72 
TCGA-BR-A4J2 TCGA-BR-A4J4 TCGA-BR-A4J5 TCGA-BR-A4J6 TCGA-BR-A4J8 TCGA-BR-A4J9 
        0.79         0.53         0.43         0.13         0.23         0.10 
TCGA-BR-A4PF TCGA-BR-A4QI TCGA-BR-A4QL TCGA-CD-5798 TCGA-CD-5799 TCGA-CD-5800 
        0.72         0.49         2.24         0.82         0.69         0.36 
TCGA-CD-5801 TCGA-CD-5802 TCGA-CD-5803 TCGA-CG-4300 TCGA-CG-4301 TCGA-CG-4304 
        0.49         0.30         0.07        20.02         3.02        27.02 
TCGA-CG-4305 TCGA-CG-4306 TCGA-CG-4436 TCGA-CG-4437 TCGA-CG-4438 TCGA-CG-4440 
       15.95         1.02        52.96         8.05        54.05         4.01 
TCGA-CG-4441 TCGA-CG-4443 TCGA-CG-4444 TCGA-CG-4449 TCGA-CG-4455 TCGA-CG-4462 
       14.01        29.98        47.05        19.07        12.03         1.02 
TCGA-CG-4465 TCGA-CG-4466 TCGA-CG-4469 TCGA-CG-4472 TCGA-CG-4477 TCGA-CG-5716 
        8.98        18.94         7.07        12.00         1.02         1.02 
TCGA-CG-5717 TCGA-CG-5718 TCGA-CG-5719 TCGA-CG-5720 TCGA-CG-5721 TCGA-CG-5723 
        6.94         1.02         1.02         0.99         5.98        70.06 
TCGA-CG-5724 TCGA-CG-5725 TCGA-CG-5726 TCGA-CG-5727 TCGA-CG-5728 TCGA-CG-5732 
       12.03        15.02        28.96        31.04        65.10        55.04 
TCGA-CG-5733 TCGA-CG-5734 TCGA-D7-5578 TCGA-D7-5579 TCGA-D7-6519 TCGA-D7-6520 
       21.07         7.99         3.58         4.54        15.65         9.63 
TCGA-D7-6522 TCGA-D7-6524 TCGA-D7-6525 TCGA-D7-6526 TCGA-D7-6527 TCGA-D7-6528 
        6.90         0.69         5.95         6.61         4.14         1.68 
TCGA-D7-6815 TCGA-D7-6817 TCGA-D7-6818 TCGA-D7-6820 TCGA-D7-6822 TCGA-EQ-5647 
        3.65         4.70         4.04         2.93         4.27         0.62 
TCGA-EQ-8122 TCGA-F1-6177 TCGA-F1-6874 TCGA-F1-6875 TCGA-FP-7735 TCGA-FP-7829 
        7.79         6.54         2.01        72.23         0.39         0.20 
TCGA-FP-7916 TCGA-FP-7998 TCGA-FP-8099 TCGA-FP-8209 TCGA-FP-8210 TCGA-FP-8631 
        3.02         3.58         1.02        59.05         5.03         0.56 
TCGA-HJ-7597 TCGA-IN-7806 TCGA-IN-7808 TCGA-IP-7968 
       26.43         6.87         3.55         2.53 

      19P GAIN CNV 19P GAIN WILD-TYPE 
              0.95               0.07 
      19P GAIN CNV 19P GAIN WILD-TYPE 
             21.99              72.23 
      19P GAIN CNV 19P GAIN WILD-TYPE 
              8.19               1.22 
[1] "0.9 - 22.0 (8.2)" "0.1 - 72.2 (1.2)"
        TCGA-B7-5816         TCGA-B7-5818         TCGA-BR-6452 
"19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" 
        TCGA-BR-6455         TCGA-BR-6457         TCGA-BR-6458 
"19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" 
        TCGA-BR-6563         TCGA-BR-6564         TCGA-BR-6565 
"19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" 
        TCGA-BR-6566         TCGA-BR-6705         TCGA-BR-6706 
"19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" 
        TCGA-BR-6707         TCGA-BR-6709         TCGA-BR-6710 
"19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" 
        TCGA-BR-6801         TCGA-BR-6802         TCGA-BR-6803 
"19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" 
        TCGA-BR-6852         TCGA-BR-7196         TCGA-BR-7197 
"19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" 
        TCGA-BR-7703         TCGA-BR-7704         TCGA-BR-7707 
"19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" 
        TCGA-BR-7715         TCGA-BR-7716         TCGA-BR-7717 
"19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" 
        TCGA-BR-7722         TCGA-BR-7723         TCGA-BR-7851 
"19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" 
        TCGA-BR-7901         TCGA-BR-7957         TCGA-BR-7958 
"19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" 
        TCGA-BR-7959         TCGA-BR-8059         TCGA-BR-8060 
"19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" 
        TCGA-BR-8077         TCGA-BR-8078         TCGA-BR-8080 
"19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" 
        TCGA-BR-8081         TCGA-BR-8284         TCGA-BR-8285 
"19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" 
        TCGA-BR-8286         TCGA-BR-8289         TCGA-BR-8291 
"19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" 
        TCGA-BR-8295         TCGA-BR-8296         TCGA-BR-8297 
"19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" 
        TCGA-BR-8592         TCGA-BR-A4IU         TCGA-BR-A4IV 
"19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" 
        TCGA-BR-A4IY         TCGA-BR-A4IZ         TCGA-BR-A4J1 
"19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" 
        TCGA-BR-A4J2         TCGA-BR-A4J4         TCGA-BR-A4J5 
"19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" 
        TCGA-BR-A4J6         TCGA-BR-A4J8         TCGA-BR-A4J9 
"19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" 
        TCGA-BR-A4PF         TCGA-BR-A4QI         TCGA-BR-A4QL 
"19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" 
        TCGA-CD-5798         TCGA-CD-5799         TCGA-CD-5800 
"19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" 
        TCGA-CD-5801         TCGA-CD-5802         TCGA-CD-5803 
"19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" 
        TCGA-CG-4300         TCGA-CG-4301         TCGA-CG-4304 
"19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" 
        TCGA-CG-4305         TCGA-CG-4306         TCGA-CG-4436 
"19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" 
        TCGA-CG-4437         TCGA-CG-4438         TCGA-CG-4440 
"19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" 
        TCGA-CG-4441         TCGA-CG-4443         TCGA-CG-4444 
"19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" 
        TCGA-CG-4449         TCGA-CG-4455         TCGA-CG-4460 
"19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE"       "19P GAIN CNV" 
        TCGA-CG-4462         TCGA-CG-4465         TCGA-CG-4466 
"19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" 
        TCGA-CG-4469         TCGA-CG-4472         TCGA-CG-4474 
"19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE"       "19P GAIN CNV" 
        TCGA-CG-4477         TCGA-CG-5716         TCGA-CG-5717 
"19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" 
        TCGA-CG-5718         TCGA-CG-5719         TCGA-CG-5720 
"19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" 
        TCGA-CG-5721         TCGA-CG-5722         TCGA-CG-5723 
"19P GAIN WILD-TYPE"       "19P GAIN CNV" "19P GAIN WILD-TYPE" 
        TCGA-CG-5724         TCGA-CG-5725         TCGA-CG-5726 
"19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" 
        TCGA-CG-5727         TCGA-CG-5728         TCGA-CG-5730 
"19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE"       "19P GAIN CNV" 
        TCGA-CG-5732         TCGA-CG-5733         TCGA-CG-5734 
"19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" 
        TCGA-D7-5577         TCGA-D7-5578         TCGA-D7-5579 
      "19P GAIN CNV" "19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" 
        TCGA-D7-6518         TCGA-D7-6519         TCGA-D7-6520 
      "19P GAIN CNV" "19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" 
        TCGA-D7-6521         TCGA-D7-6522         TCGA-D7-6524 
      "19P GAIN CNV" "19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" 
        TCGA-D7-6525         TCGA-D7-6526         TCGA-D7-6527 
"19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" 
        TCGA-D7-6528         TCGA-D7-6815         TCGA-D7-6817 
"19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" 
        TCGA-D7-6818         TCGA-D7-6820         TCGA-D7-6822 
"19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" 
        TCGA-EQ-5647         TCGA-EQ-8122         TCGA-F1-6177 
"19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" 
        TCGA-F1-6874         TCGA-F1-6875         TCGA-FP-7735 
"19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" 
        TCGA-FP-7829         TCGA-FP-7916         TCGA-FP-7998 
"19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" 
        TCGA-FP-8099         TCGA-FP-8209         TCGA-FP-8210 
"19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" 
        TCGA-FP-8631         TCGA-HJ-7597         TCGA-IN-7806 
"19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" 
        TCGA-IN-7808         TCGA-IP-7968 
"19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" 
        TCGA-B7-5816         TCGA-B7-5818         TCGA-BR-6452 
"19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" 
        TCGA-BR-6455         TCGA-BR-6457         TCGA-BR-6458 
"19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" 
        TCGA-BR-6563         TCGA-BR-6564         TCGA-BR-6565 
"19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" 
        TCGA-BR-6566         TCGA-BR-6705         TCGA-BR-6706 
"19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" 
        TCGA-BR-6707         TCGA-BR-6709         TCGA-BR-6710 
"19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" 
        TCGA-BR-6801         TCGA-BR-6802         TCGA-BR-6803 
"19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" 
        TCGA-BR-6852         TCGA-BR-7196         TCGA-BR-7197 
"19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" 
        TCGA-BR-7703         TCGA-BR-7704         TCGA-BR-7707 
"19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" 
        TCGA-BR-7715         TCGA-BR-7716         TCGA-BR-7717 
"19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" 
        TCGA-BR-7722         TCGA-BR-7723         TCGA-BR-7851 
"19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" 
        TCGA-BR-7901         TCGA-BR-7957         TCGA-BR-7958 
"19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" 
        TCGA-BR-7959         TCGA-BR-8059         TCGA-BR-8060 
"19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" 
        TCGA-BR-8077         TCGA-BR-8078         TCGA-BR-8080 
"19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" 
        TCGA-BR-8081         TCGA-BR-8284         TCGA-BR-8285 
"19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" 
        TCGA-BR-8286         TCGA-BR-8289         TCGA-BR-8291 
"19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" 
        TCGA-BR-8295         TCGA-BR-8296         TCGA-BR-8297 
"19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" 
        TCGA-BR-8592         TCGA-BR-A4IU         TCGA-BR-A4IV 
"19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" 
        TCGA-BR-A4IY         TCGA-BR-A4IZ         TCGA-BR-A4J1 
"19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" 
        TCGA-BR-A4J2         TCGA-BR-A4J4         TCGA-BR-A4J5 
"19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" 
        TCGA-BR-A4J6         TCGA-BR-A4J8         TCGA-BR-A4J9 
"19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" 
        TCGA-BR-A4PF         TCGA-BR-A4QI         TCGA-BR-A4QL 
"19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" 
        TCGA-CD-5798         TCGA-CD-5799         TCGA-CD-5800 
"19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" 
        TCGA-CD-5801         TCGA-CD-5802         TCGA-CD-5803 
"19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" 
        TCGA-CG-4300         TCGA-CG-4301         TCGA-CG-4304 
"19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" 
        TCGA-CG-4305         TCGA-CG-4306         TCGA-CG-4436 
"19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" 
        TCGA-CG-4437         TCGA-CG-4438         TCGA-CG-4440 
"19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" 
        TCGA-CG-4441         TCGA-CG-4443         TCGA-CG-4444 
"19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" 
        TCGA-CG-4449         TCGA-CG-4455         TCGA-CG-4460 
"19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE"       "19P GAIN CNV" 
        TCGA-CG-4462         TCGA-CG-4465         TCGA-CG-4466 
"19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" 
        TCGA-CG-4469         TCGA-CG-4472         TCGA-CG-4474 
"19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE"       "19P GAIN CNV" 
        TCGA-CG-4477         TCGA-CG-5716         TCGA-CG-5717 
"19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" 
        TCGA-CG-5718         TCGA-CG-5719         TCGA-CG-5720 
"19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" 
        TCGA-CG-5721         TCGA-CG-5722         TCGA-CG-5723 
"19P GAIN WILD-TYPE"       "19P GAIN CNV" "19P GAIN WILD-TYPE" 
        TCGA-CG-5724         TCGA-CG-5725         TCGA-CG-5726 
"19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" 
        TCGA-CG-5727         TCGA-CG-5728         TCGA-CG-5730 
"19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE"       "19P GAIN CNV" 
        TCGA-CG-5732         TCGA-CG-5733         TCGA-CG-5734 
"19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" 
        TCGA-D7-5577         TCGA-D7-5578         TCGA-D7-5579 
      "19P GAIN CNV" "19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" 
        TCGA-D7-6518         TCGA-D7-6519         TCGA-D7-6520 
      "19P GAIN CNV" "19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" 
        TCGA-D7-6521         TCGA-D7-6522         TCGA-D7-6524 
      "19P GAIN CNV" "19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" 
        TCGA-D7-6525         TCGA-D7-6526         TCGA-D7-6527 
"19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" 
        TCGA-D7-6528         TCGA-D7-6815         TCGA-D7-6817 
"19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" 
        TCGA-D7-6818         TCGA-D7-6820         TCGA-D7-6822 
"19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" 
        TCGA-EQ-5647         TCGA-EQ-8122         TCGA-F1-6177 
"19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" 
        TCGA-F1-6874         TCGA-F1-6875         TCGA-FP-7735 
"19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" 
        TCGA-FP-7829         TCGA-FP-7916         TCGA-FP-7998 
"19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" 
        TCGA-FP-8099         TCGA-FP-8209         TCGA-FP-8210 
"19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" 
        TCGA-FP-8631         TCGA-HJ-7597         TCGA-IN-7806 
"19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" 
        TCGA-IN-7808         TCGA-IP-7968 
"19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" 
        TCGA-B7-5816         TCGA-B7-5818         TCGA-BR-6452 
"19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" 
        TCGA-BR-6455         TCGA-BR-6457         TCGA-BR-6458 
"19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" 
        TCGA-BR-6563         TCGA-BR-6564         TCGA-BR-6565 
"19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" 
        TCGA-BR-6566         TCGA-BR-6705         TCGA-BR-6706 
"19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" 
        TCGA-BR-6707         TCGA-BR-6709         TCGA-BR-6710 
"19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" 
        TCGA-BR-6801         TCGA-BR-6802         TCGA-BR-6803 
"19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" 
        TCGA-BR-6852         TCGA-BR-7196         TCGA-BR-7197 
"19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" 
        TCGA-BR-7703         TCGA-BR-7704         TCGA-BR-7707 
"19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" 
        TCGA-BR-7715         TCGA-BR-7716         TCGA-BR-7717 
"19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" 
        TCGA-BR-7722         TCGA-BR-7723         TCGA-BR-7851 
"19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" 
        TCGA-BR-7901         TCGA-BR-7957         TCGA-BR-7958 
"19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" 
        TCGA-BR-7959         TCGA-BR-8059         TCGA-BR-8060 
"19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" 
        TCGA-BR-8077         TCGA-BR-8078         TCGA-BR-8080 
"19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" 
        TCGA-BR-8081         TCGA-BR-8284         TCGA-BR-8285 
"19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" 
        TCGA-BR-8286         TCGA-BR-8289         TCGA-BR-8291 
"19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" 
        TCGA-BR-8295         TCGA-BR-8296         TCGA-BR-8297 
"19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" 
        TCGA-BR-8592         TCGA-BR-A4IU         TCGA-BR-A4IV 
"19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" 
        TCGA-BR-A4IY         TCGA-BR-A4IZ         TCGA-BR-A4J1 
"19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" 
        TCGA-BR-A4J2         TCGA-BR-A4J4         TCGA-BR-A4J5 
"19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" 
        TCGA-BR-A4J6         TCGA-BR-A4J8         TCGA-BR-A4J9 
"19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" 
        TCGA-BR-A4PF         TCGA-BR-A4QI         TCGA-BR-A4QL 
"19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" 
        TCGA-CD-5798         TCGA-CD-5799         TCGA-CD-5800 
"19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" 
        TCGA-CD-5801         TCGA-CD-5802         TCGA-CD-5803 
"19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" 
        TCGA-CG-4300         TCGA-CG-4301         TCGA-CG-4304 
"19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" 
        TCGA-CG-4305         TCGA-CG-4306         TCGA-CG-4436 
"19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" 
        TCGA-CG-4437         TCGA-CG-4438         TCGA-CG-4440 
"19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" 
        TCGA-CG-4441         TCGA-CG-4443         TCGA-CG-4444 
"19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" 
        TCGA-CG-4449         TCGA-CG-4455         TCGA-CG-4460 
"19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE"       "19P GAIN CNV" 
        TCGA-CG-4462         TCGA-CG-4465         TCGA-CG-4466 
"19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" 
        TCGA-CG-4469         TCGA-CG-4472         TCGA-CG-4474 
"19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE"       "19P GAIN CNV" 
        TCGA-CG-4477         TCGA-CG-5716         TCGA-CG-5717 
"19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" 
        TCGA-CG-5718         TCGA-CG-5719         TCGA-CG-5720 
"19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" 
        TCGA-CG-5721         TCGA-CG-5722         TCGA-CG-5723 
"19P GAIN WILD-TYPE"       "19P GAIN CNV" "19P GAIN WILD-TYPE" 
        TCGA-CG-5724         TCGA-CG-5725         TCGA-CG-5726 
"19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" 
        TCGA-CG-5727         TCGA-CG-5728         TCGA-CG-5730 
"19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE"       "19P GAIN CNV" 
        TCGA-CG-5732         TCGA-CG-5733         TCGA-CG-5734 
"19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" 
        TCGA-D7-5577         TCGA-D7-5578         TCGA-D7-5579 
      "19P GAIN CNV" "19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" 
        TCGA-D7-6518         TCGA-D7-6519         TCGA-D7-6520 
      "19P GAIN CNV" "19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" 
        TCGA-D7-6521         TCGA-D7-6522         TCGA-D7-6524 
      "19P GAIN CNV" "19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" 
        TCGA-D7-6525         TCGA-D7-6526         TCGA-D7-6527 
"19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" 
        TCGA-D7-6528         TCGA-D7-6815         TCGA-D7-6817 
"19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" 
        TCGA-D7-6818         TCGA-D7-6820         TCGA-D7-6822 
"19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" 
        TCGA-EQ-5647         TCGA-EQ-8122         TCGA-F1-6177 
"19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" 
        TCGA-F1-6874         TCGA-F1-6875         TCGA-FP-7735 
"19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" 
        TCGA-FP-7829         TCGA-FP-7916         TCGA-FP-7998 
"19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" 
        TCGA-FP-8099         TCGA-FP-8209         TCGA-FP-8210 
"19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" 
        TCGA-FP-8631         TCGA-HJ-7597         TCGA-IN-7806 
"19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" 
        TCGA-IN-7808         TCGA-IP-7968 
"19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" 
[1] "hr=" "1.2"
D33V2, continuous
D33V3, binary
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  19P GAIN CNV          8    2
  19P GAIN WILD-TYPE   64  106
        clus
vv       19P GAIN CNV 19P GAIN WILD-TYPE
  FEMALE            8                 64
  MALE              2                106
                    vv
clus                 STOMACH  ADENOCARCINOMA  DIFFUSE TYPE
  19P GAIN CNV                                           0
  19P GAIN WILD-TYPE                                    10
                    vv
clus                 STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  19P GAIN CNV                                                            0
  19P GAIN WILD-TYPE                                                     16
                    vv
clus                 STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  19P GAIN CNV                                                                       0
  19P GAIN WILD-TYPE                                                                 8
                    vv
clus                 STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE
  19P GAIN CNV                                                              0
  19P GAIN WILD-TYPE                                                        3
                    vv
clus                 STOMACH ADENOCARCINOMA  SIGNET RING TYPE
  19P GAIN CNV                                              0
  19P GAIN WILD-TYPE                                        1
                    vv
clus                 STOMACH ADENOCARCINOMA - DIFFUSE TYPE
  19P GAIN CNV                                           3
  19P GAIN WILD-TYPE                                    13
                    vv
clus                 STOMACH ADENOCARCINOMA - NOT OTHERWISE SPECIFIED (NOS)
  19P GAIN CNV                                                            3
  19P GAIN WILD-TYPE                                                     70
                    vv
clus                 STOMACH INTESTINAL ADENOCARCINOMA - MUCINOUS TYPE
  19P GAIN CNV                                                       0
  19P GAIN WILD-TYPE                                                 7
                    vv
clus                 STOMACH INTESTINAL ADENOCARCINOMA - PAPILLARY TYPE
  19P GAIN CNV                                                        0
  19P GAIN WILD-TYPE                                                  3
                    vv
clus                 STOMACH INTESTINAL ADENOCARCINOMA - TUBULAR TYPE
  19P GAIN CNV                                                      1
  19P GAIN WILD-TYPE                                                9
                    vv
clus                 STOMACH INTESTINAL ADENOCARCINOMA - TYPE NOT OTHERWISE SPECIFIED (NOS)
  19P GAIN CNV                                                                            3
  19P GAIN WILD-TYPE                                                                     25
D33V4, multiclass
                    vv
clus                 T1 T2 T3 T4
  19P GAIN CNV        0  5  3  2
  19P GAIN WILD-TYPE  6 47 53 16
D33V5, multiclass
    clus
vv   19P GAIN CNV 19P GAIN WILD-TYPE
  T1            0                  6
  T2            5                 47
  T3            3                 53
  T4            2                 16
                    vv
clus                 N0 N1 N2 N3
  19P GAIN CNV        0  4  3  2
  19P GAIN WILD-TYPE 44 45 20 13
D33V6, multiclass
    clus
vv   19P GAIN CNV 19P GAIN WILD-TYPE
  N0            0                 44
  N1            4                 45
  N2            3                 20
  N3            2                 13
                    vv
clus                  M0  M1  MX
  19P GAIN CNV         6   4   0
  19P GAIN WILD-TYPE 112  12   8
D33V7, multiclass
    clus
vv   19P GAIN CNV 19P GAIN WILD-TYPE
  M0            6                112
  M1            4                 12
  MX            0                  8
                    vv
clus                  I II III IV
  19P GAIN CNV        0  1   3  5
  19P GAIN WILD-TYPE 24 36  36 21
D33V8, multiclass
     clus
vv    19P GAIN CNV 19P GAIN WILD-TYPE
  I              0                 24
  II             1                 36
  III            3                 36
  IV             5                 21
D33V9, binary
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  19P GAIN CNV          0   10
  19P GAIN WILD-TYPE    5  165
     clus
vv    19P GAIN CNV 19P GAIN WILD-TYPE
  NO             0                  5
  YES           10                165
                    vv
clus                  R0  R1  R2  RX
  19P GAIN CNV         3   1   4   2
  19P GAIN WILD-TYPE 122   6   8  23
D33V10, multiclass
    clus
vv   19P GAIN CNV 19P GAIN WILD-TYPE
  R0            3                122
  R1            1                  6
  R2            4                  8
  RX            2                 23
D33V11, continuous

Clustering(34) Variable = 19q gain
D34V1, survival
                    sevent
clus2                  0   1
  19Q GAIN CNV        12   2
  19Q GAIN WILD-TYPE 112  17
      19Q GAIN CNV 19Q GAIN WILD-TYPE 
                14                129 
      19Q GAIN CNV 19Q GAIN WILD-TYPE 
                 2                 17 
$`19Q GAIN CNV`
TCGA-BR-7716 TCGA-BR-8286 TCGA-CG-4438 TCGA-CG-4460 TCGA-CG-4474 TCGA-CG-5722 
        0.82         0.43        54.05        21.99         1.02         0.95 
TCGA-CG-5730 TCGA-D7-5577 TCGA-D7-6518 TCGA-D7-6521 TCGA-D7-6822 TCGA-EQ-8122 
        4.01         8.65         9.80         8.19         4.27         7.79 
TCGA-F1-6875 TCGA-FP-7916 
       72.23         3.02 

$`19Q GAIN WILD-TYPE`
TCGA-B7-5816 TCGA-B7-5818 TCGA-BR-6452 TCGA-BR-6455 TCGA-BR-6457 TCGA-BR-6458 
        5.62         0.10         0.95         1.41         1.35         1.35 
TCGA-BR-6563 TCGA-BR-6564 TCGA-BR-6565 TCGA-BR-6566 TCGA-BR-6705 TCGA-BR-6706 
        0.85         0.82         0.62         0.62         1.71         2.17 
TCGA-BR-6707 TCGA-BR-6709 TCGA-BR-6710 TCGA-BR-6801 TCGA-BR-6802 TCGA-BR-6803 
        0.99         1.22         0.66         1.12         0.76         0.66 
TCGA-BR-6852 TCGA-BR-7196 TCGA-BR-7197 TCGA-BR-7703 TCGA-BR-7704 TCGA-BR-7707 
        0.26         1.22         1.48         0.46         1.25         0.13 
TCGA-BR-7715 TCGA-BR-7717 TCGA-BR-7722 TCGA-BR-7723 TCGA-BR-7851 TCGA-BR-7901 
        1.05         0.69         0.16         4.54         0.99         0.95 
TCGA-BR-7957 TCGA-BR-7958 TCGA-BR-7959 TCGA-BR-8059 TCGA-BR-8060 TCGA-BR-8077 
        0.69         0.16         1.08         0.82         1.32         0.69 
TCGA-BR-8078 TCGA-BR-8080 TCGA-BR-8081 TCGA-BR-8284 TCGA-BR-8285 TCGA-BR-8289 
        0.95         0.49         0.46         0.72         0.26         0.26 
TCGA-BR-8291 TCGA-BR-8295 TCGA-BR-8296 TCGA-BR-8297 TCGA-BR-8592 TCGA-BR-A4IU 
        1.18         1.55         1.48         0.76         0.20         0.59 
TCGA-BR-A4IV TCGA-BR-A4IY TCGA-BR-A4IZ TCGA-BR-A4J1 TCGA-BR-A4J2 TCGA-BR-A4J4 
        0.92         0.39         0.79         0.72         0.79         0.53 
TCGA-BR-A4J5 TCGA-BR-A4J6 TCGA-BR-A4J8 TCGA-BR-A4J9 TCGA-BR-A4PF TCGA-BR-A4QI 
        0.43         0.13         0.23         0.10         0.72         0.49 
TCGA-BR-A4QL TCGA-CD-5798 TCGA-CD-5799 TCGA-CD-5800 TCGA-CD-5801 TCGA-CD-5802 
        2.24         0.82         0.69         0.36         0.49         0.30 
TCGA-CD-5803 TCGA-CG-4300 TCGA-CG-4301 TCGA-CG-4304 TCGA-CG-4305 TCGA-CG-4306 
        0.07        20.02         3.02        27.02        15.95         1.02 
TCGA-CG-4436 TCGA-CG-4437 TCGA-CG-4440 TCGA-CG-4441 TCGA-CG-4443 TCGA-CG-4444 
       52.96         8.05         4.01        14.01        29.98        47.05 
TCGA-CG-4449 TCGA-CG-4455 TCGA-CG-4462 TCGA-CG-4465 TCGA-CG-4466 TCGA-CG-4469 
       19.07        12.03         1.02         8.98        18.94         7.07 
TCGA-CG-4472 TCGA-CG-4477 TCGA-CG-5716 TCGA-CG-5717 TCGA-CG-5718 TCGA-CG-5719 
       12.00         1.02         1.02         6.94         1.02         1.02 
TCGA-CG-5720 TCGA-CG-5721 TCGA-CG-5723 TCGA-CG-5724 TCGA-CG-5725 TCGA-CG-5726 
        0.99         5.98        70.06        12.03        15.02        28.96 
TCGA-CG-5727 TCGA-CG-5728 TCGA-CG-5732 TCGA-CG-5733 TCGA-CG-5734 TCGA-D7-5578 
       31.04        65.10        55.04        21.07         7.99         3.58 
TCGA-D7-5579 TCGA-D7-6519 TCGA-D7-6520 TCGA-D7-6522 TCGA-D7-6524 TCGA-D7-6525 
        4.54        15.65         9.63         6.90         0.69         5.95 
TCGA-D7-6526 TCGA-D7-6527 TCGA-D7-6528 TCGA-D7-6815 TCGA-D7-6817 TCGA-D7-6818 
        6.61         4.14         1.68         3.65         4.70         4.04 
TCGA-D7-6820 TCGA-EQ-5647 TCGA-F1-6177 TCGA-F1-6874 TCGA-FP-7735 TCGA-FP-7829 
        2.93         0.62         6.54         2.01         0.39         0.20 
TCGA-FP-7998 TCGA-FP-8099 TCGA-FP-8209 TCGA-FP-8210 TCGA-FP-8631 TCGA-HJ-7597 
        3.58         1.02        59.05         5.03         0.56        26.43 
TCGA-IN-7806 TCGA-IN-7808 TCGA-IP-7968 
        6.87         3.55         2.53 

      19Q GAIN CNV 19Q GAIN WILD-TYPE 
              0.43               0.07 
      19Q GAIN CNV 19Q GAIN WILD-TYPE 
             72.23              70.06 
      19Q GAIN CNV 19Q GAIN WILD-TYPE 
              6.03               1.18 
[1] "0.4 - 72.2 (6.0)" "0.1 - 70.1 (1.2)"
        TCGA-B7-5816         TCGA-B7-5818         TCGA-BR-6452 
"19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" 
        TCGA-BR-6455         TCGA-BR-6457         TCGA-BR-6458 
"19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" 
        TCGA-BR-6563         TCGA-BR-6564         TCGA-BR-6565 
"19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" 
        TCGA-BR-6566         TCGA-BR-6705         TCGA-BR-6706 
"19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" 
        TCGA-BR-6707         TCGA-BR-6709         TCGA-BR-6710 
"19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" 
        TCGA-BR-6801         TCGA-BR-6802         TCGA-BR-6803 
"19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" 
        TCGA-BR-6852         TCGA-BR-7196         TCGA-BR-7197 
"19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" 
        TCGA-BR-7703         TCGA-BR-7704         TCGA-BR-7707 
"19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" 
        TCGA-BR-7715         TCGA-BR-7716         TCGA-BR-7717 
"19Q GAIN WILD-TYPE"       "19Q GAIN CNV" "19Q GAIN WILD-TYPE" 
        TCGA-BR-7722         TCGA-BR-7723         TCGA-BR-7851 
"19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" 
        TCGA-BR-7901         TCGA-BR-7957         TCGA-BR-7958 
"19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" 
        TCGA-BR-7959         TCGA-BR-8059         TCGA-BR-8060 
"19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" 
        TCGA-BR-8077         TCGA-BR-8078         TCGA-BR-8080 
"19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" 
        TCGA-BR-8081         TCGA-BR-8284         TCGA-BR-8285 
"19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" 
        TCGA-BR-8286         TCGA-BR-8289         TCGA-BR-8291 
      "19Q GAIN CNV" "19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" 
        TCGA-BR-8295         TCGA-BR-8296         TCGA-BR-8297 
"19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" 
        TCGA-BR-8592         TCGA-BR-A4IU         TCGA-BR-A4IV 
"19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" 
        TCGA-BR-A4IY         TCGA-BR-A4IZ         TCGA-BR-A4J1 
"19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" 
        TCGA-BR-A4J2         TCGA-BR-A4J4         TCGA-BR-A4J5 
"19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" 
        TCGA-BR-A4J6         TCGA-BR-A4J8         TCGA-BR-A4J9 
"19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" 
        TCGA-BR-A4PF         TCGA-BR-A4QI         TCGA-BR-A4QL 
"19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" 
        TCGA-CD-5798         TCGA-CD-5799         TCGA-CD-5800 
"19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" 
        TCGA-CD-5801         TCGA-CD-5802         TCGA-CD-5803 
"19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" 
        TCGA-CG-4300         TCGA-CG-4301         TCGA-CG-4304 
"19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" 
        TCGA-CG-4305         TCGA-CG-4306         TCGA-CG-4436 
"19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" 
        TCGA-CG-4437         TCGA-CG-4438         TCGA-CG-4440 
"19Q GAIN WILD-TYPE"       "19Q GAIN CNV" "19Q GAIN WILD-TYPE" 
        TCGA-CG-4441         TCGA-CG-4443         TCGA-CG-4444 
"19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" 
        TCGA-CG-4449         TCGA-CG-4455         TCGA-CG-4460 
"19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE"       "19Q GAIN CNV" 
        TCGA-CG-4462         TCGA-CG-4465         TCGA-CG-4466 
"19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" 
        TCGA-CG-4469         TCGA-CG-4472         TCGA-CG-4474 
"19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE"       "19Q GAIN CNV" 
        TCGA-CG-4477         TCGA-CG-5716         TCGA-CG-5717 
"19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" 
        TCGA-CG-5718         TCGA-CG-5719         TCGA-CG-5720 
"19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" 
        TCGA-CG-5721         TCGA-CG-5722         TCGA-CG-5723 
"19Q GAIN WILD-TYPE"       "19Q GAIN CNV" "19Q GAIN WILD-TYPE" 
        TCGA-CG-5724         TCGA-CG-5725         TCGA-CG-5726 
"19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" 
        TCGA-CG-5727         TCGA-CG-5728         TCGA-CG-5730 
"19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE"       "19Q GAIN CNV" 
        TCGA-CG-5732         TCGA-CG-5733         TCGA-CG-5734 
"19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" 
        TCGA-D7-5577         TCGA-D7-5578         TCGA-D7-5579 
      "19Q GAIN CNV" "19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" 
        TCGA-D7-6518         TCGA-D7-6519         TCGA-D7-6520 
      "19Q GAIN CNV" "19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" 
        TCGA-D7-6521         TCGA-D7-6522         TCGA-D7-6524 
      "19Q GAIN CNV" "19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" 
        TCGA-D7-6525         TCGA-D7-6526         TCGA-D7-6527 
"19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" 
        TCGA-D7-6528         TCGA-D7-6815         TCGA-D7-6817 
"19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" 
        TCGA-D7-6818         TCGA-D7-6820         TCGA-D7-6822 
"19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE"       "19Q GAIN CNV" 
        TCGA-EQ-5647         TCGA-EQ-8122         TCGA-F1-6177 
"19Q GAIN WILD-TYPE"       "19Q GAIN CNV" "19Q GAIN WILD-TYPE" 
        TCGA-F1-6874         TCGA-F1-6875         TCGA-FP-7735 
"19Q GAIN WILD-TYPE"       "19Q GAIN CNV" "19Q GAIN WILD-TYPE" 
        TCGA-FP-7829         TCGA-FP-7916         TCGA-FP-7998 
"19Q GAIN WILD-TYPE"       "19Q GAIN CNV" "19Q GAIN WILD-TYPE" 
        TCGA-FP-8099         TCGA-FP-8209         TCGA-FP-8210 
"19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" 
        TCGA-FP-8631         TCGA-HJ-7597         TCGA-IN-7806 
"19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" 
        TCGA-IN-7808         TCGA-IP-7968 
"19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" 
        TCGA-B7-5816         TCGA-B7-5818         TCGA-BR-6452 
"19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" 
        TCGA-BR-6455         TCGA-BR-6457         TCGA-BR-6458 
"19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" 
        TCGA-BR-6563         TCGA-BR-6564         TCGA-BR-6565 
"19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" 
        TCGA-BR-6566         TCGA-BR-6705         TCGA-BR-6706 
"19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" 
        TCGA-BR-6707         TCGA-BR-6709         TCGA-BR-6710 
"19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" 
        TCGA-BR-6801         TCGA-BR-6802         TCGA-BR-6803 
"19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" 
        TCGA-BR-6852         TCGA-BR-7196         TCGA-BR-7197 
"19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" 
        TCGA-BR-7703         TCGA-BR-7704         TCGA-BR-7707 
"19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" 
        TCGA-BR-7715         TCGA-BR-7716         TCGA-BR-7717 
"19Q GAIN WILD-TYPE"       "19Q GAIN CNV" "19Q GAIN WILD-TYPE" 
        TCGA-BR-7722         TCGA-BR-7723         TCGA-BR-7851 
"19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" 
        TCGA-BR-7901         TCGA-BR-7957         TCGA-BR-7958 
"19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" 
        TCGA-BR-7959         TCGA-BR-8059         TCGA-BR-8060 
"19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" 
        TCGA-BR-8077         TCGA-BR-8078         TCGA-BR-8080 
"19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" 
        TCGA-BR-8081         TCGA-BR-8284         TCGA-BR-8285 
"19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" 
        TCGA-BR-8286         TCGA-BR-8289         TCGA-BR-8291 
      "19Q GAIN CNV" "19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" 
        TCGA-BR-8295         TCGA-BR-8296         TCGA-BR-8297 
"19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" 
        TCGA-BR-8592         TCGA-BR-A4IU         TCGA-BR-A4IV 
"19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" 
        TCGA-BR-A4IY         TCGA-BR-A4IZ         TCGA-BR-A4J1 
"19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" 
        TCGA-BR-A4J2         TCGA-BR-A4J4         TCGA-BR-A4J5 
"19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" 
        TCGA-BR-A4J6         TCGA-BR-A4J8         TCGA-BR-A4J9 
"19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" 
        TCGA-BR-A4PF         TCGA-BR-A4QI         TCGA-BR-A4QL 
"19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" 
        TCGA-CD-5798         TCGA-CD-5799         TCGA-CD-5800 
"19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" 
        TCGA-CD-5801         TCGA-CD-5802         TCGA-CD-5803 
"19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" 
        TCGA-CG-4300         TCGA-CG-4301         TCGA-CG-4304 
"19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" 
        TCGA-CG-4305         TCGA-CG-4306         TCGA-CG-4436 
"19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" 
        TCGA-CG-4437         TCGA-CG-4438         TCGA-CG-4440 
"19Q GAIN WILD-TYPE"       "19Q GAIN CNV" "19Q GAIN WILD-TYPE" 
        TCGA-CG-4441         TCGA-CG-4443         TCGA-CG-4444 
"19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" 
        TCGA-CG-4449         TCGA-CG-4455         TCGA-CG-4460 
"19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE"       "19Q GAIN CNV" 
        TCGA-CG-4462         TCGA-CG-4465         TCGA-CG-4466 
"19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" 
        TCGA-CG-4469         TCGA-CG-4472         TCGA-CG-4474 
"19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE"       "19Q GAIN CNV" 
        TCGA-CG-4477         TCGA-CG-5716         TCGA-CG-5717 
"19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" 
        TCGA-CG-5718         TCGA-CG-5719         TCGA-CG-5720 
"19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" 
        TCGA-CG-5721         TCGA-CG-5722         TCGA-CG-5723 
"19Q GAIN WILD-TYPE"       "19Q GAIN CNV" "19Q GAIN WILD-TYPE" 
        TCGA-CG-5724         TCGA-CG-5725         TCGA-CG-5726 
"19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" 
        TCGA-CG-5727         TCGA-CG-5728         TCGA-CG-5730 
"19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE"       "19Q GAIN CNV" 
        TCGA-CG-5732         TCGA-CG-5733         TCGA-CG-5734 
"19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" 
        TCGA-D7-5577         TCGA-D7-5578         TCGA-D7-5579 
      "19Q GAIN CNV" "19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" 
        TCGA-D7-6518         TCGA-D7-6519         TCGA-D7-6520 
      "19Q GAIN CNV" "19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" 
        TCGA-D7-6521         TCGA-D7-6522         TCGA-D7-6524 
      "19Q GAIN CNV" "19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" 
        TCGA-D7-6525         TCGA-D7-6526         TCGA-D7-6527 
"19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" 
        TCGA-D7-6528         TCGA-D7-6815         TCGA-D7-6817 
"19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" 
        TCGA-D7-6818         TCGA-D7-6820         TCGA-D7-6822 
"19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE"       "19Q GAIN CNV" 
        TCGA-EQ-5647         TCGA-EQ-8122         TCGA-F1-6177 
"19Q GAIN WILD-TYPE"       "19Q GAIN CNV" "19Q GAIN WILD-TYPE" 
        TCGA-F1-6874         TCGA-F1-6875         TCGA-FP-7735 
"19Q GAIN WILD-TYPE"       "19Q GAIN CNV" "19Q GAIN WILD-TYPE" 
        TCGA-FP-7829         TCGA-FP-7916         TCGA-FP-7998 
"19Q GAIN WILD-TYPE"       "19Q GAIN CNV" "19Q GAIN WILD-TYPE" 
        TCGA-FP-8099         TCGA-FP-8209         TCGA-FP-8210 
"19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" 
        TCGA-FP-8631         TCGA-HJ-7597         TCGA-IN-7806 
"19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" 
        TCGA-IN-7808         TCGA-IP-7968 
"19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" 
        TCGA-B7-5816         TCGA-B7-5818         TCGA-BR-6452 
"19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" 
        TCGA-BR-6455         TCGA-BR-6457         TCGA-BR-6458 
"19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" 
        TCGA-BR-6563         TCGA-BR-6564         TCGA-BR-6565 
"19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" 
        TCGA-BR-6566         TCGA-BR-6705         TCGA-BR-6706 
"19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" 
        TCGA-BR-6707         TCGA-BR-6709         TCGA-BR-6710 
"19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" 
        TCGA-BR-6801         TCGA-BR-6802         TCGA-BR-6803 
"19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" 
        TCGA-BR-6852         TCGA-BR-7196         TCGA-BR-7197 
"19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" 
        TCGA-BR-7703         TCGA-BR-7704         TCGA-BR-7707 
"19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" 
        TCGA-BR-7715         TCGA-BR-7716         TCGA-BR-7717 
"19Q GAIN WILD-TYPE"       "19Q GAIN CNV" "19Q GAIN WILD-TYPE" 
        TCGA-BR-7722         TCGA-BR-7723         TCGA-BR-7851 
"19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" 
        TCGA-BR-7901         TCGA-BR-7957         TCGA-BR-7958 
"19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" 
        TCGA-BR-7959         TCGA-BR-8059         TCGA-BR-8060 
"19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" 
        TCGA-BR-8077         TCGA-BR-8078         TCGA-BR-8080 
"19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" 
        TCGA-BR-8081         TCGA-BR-8284         TCGA-BR-8285 
"19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" 
        TCGA-BR-8286         TCGA-BR-8289         TCGA-BR-8291 
      "19Q GAIN CNV" "19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" 
        TCGA-BR-8295         TCGA-BR-8296         TCGA-BR-8297 
"19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" 
        TCGA-BR-8592         TCGA-BR-A4IU         TCGA-BR-A4IV 
"19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" 
        TCGA-BR-A4IY         TCGA-BR-A4IZ         TCGA-BR-A4J1 
"19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" 
        TCGA-BR-A4J2         TCGA-BR-A4J4         TCGA-BR-A4J5 
"19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" 
        TCGA-BR-A4J6         TCGA-BR-A4J8         TCGA-BR-A4J9 
"19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" 
        TCGA-BR-A4PF         TCGA-BR-A4QI         TCGA-BR-A4QL 
"19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" 
        TCGA-CD-5798         TCGA-CD-5799         TCGA-CD-5800 
"19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" 
        TCGA-CD-5801         TCGA-CD-5802         TCGA-CD-5803 
"19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" 
        TCGA-CG-4300         TCGA-CG-4301         TCGA-CG-4304 
"19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" 
        TCGA-CG-4305         TCGA-CG-4306         TCGA-CG-4436 
"19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" 
        TCGA-CG-4437         TCGA-CG-4438         TCGA-CG-4440 
"19Q GAIN WILD-TYPE"       "19Q GAIN CNV" "19Q GAIN WILD-TYPE" 
        TCGA-CG-4441         TCGA-CG-4443         TCGA-CG-4444 
"19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" 
        TCGA-CG-4449         TCGA-CG-4455         TCGA-CG-4460 
"19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE"       "19Q GAIN CNV" 
        TCGA-CG-4462         TCGA-CG-4465         TCGA-CG-4466 
"19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" 
        TCGA-CG-4469         TCGA-CG-4472         TCGA-CG-4474 
"19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE"       "19Q GAIN CNV" 
        TCGA-CG-4477         TCGA-CG-5716         TCGA-CG-5717 
"19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" 
        TCGA-CG-5718         TCGA-CG-5719         TCGA-CG-5720 
"19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" 
        TCGA-CG-5721         TCGA-CG-5722         TCGA-CG-5723 
"19Q GAIN WILD-TYPE"       "19Q GAIN CNV" "19Q GAIN WILD-TYPE" 
        TCGA-CG-5724         TCGA-CG-5725         TCGA-CG-5726 
"19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" 
        TCGA-CG-5727         TCGA-CG-5728         TCGA-CG-5730 
"19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE"       "19Q GAIN CNV" 
        TCGA-CG-5732         TCGA-CG-5733         TCGA-CG-5734 
"19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" 
        TCGA-D7-5577         TCGA-D7-5578         TCGA-D7-5579 
      "19Q GAIN CNV" "19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" 
        TCGA-D7-6518         TCGA-D7-6519         TCGA-D7-6520 
      "19Q GAIN CNV" "19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" 
        TCGA-D7-6521         TCGA-D7-6522         TCGA-D7-6524 
      "19Q GAIN CNV" "19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" 
        TCGA-D7-6525         TCGA-D7-6526         TCGA-D7-6527 
"19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" 
        TCGA-D7-6528         TCGA-D7-6815         TCGA-D7-6817 
"19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" 
        TCGA-D7-6818         TCGA-D7-6820         TCGA-D7-6822 
"19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE"       "19Q GAIN CNV" 
        TCGA-EQ-5647         TCGA-EQ-8122         TCGA-F1-6177 
"19Q GAIN WILD-TYPE"       "19Q GAIN CNV" "19Q GAIN WILD-TYPE" 
        TCGA-F1-6874         TCGA-F1-6875         TCGA-FP-7735 
"19Q GAIN WILD-TYPE"       "19Q GAIN CNV" "19Q GAIN WILD-TYPE" 
        TCGA-FP-7829         TCGA-FP-7916         TCGA-FP-7998 
"19Q GAIN WILD-TYPE"       "19Q GAIN CNV" "19Q GAIN WILD-TYPE" 
        TCGA-FP-8099         TCGA-FP-8209         TCGA-FP-8210 
"19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" 
        TCGA-FP-8631         TCGA-HJ-7597         TCGA-IN-7806 
"19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" 
        TCGA-IN-7808         TCGA-IP-7968 
"19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" 
[1] "hr=" "3.4"
D34V2, continuous
D34V3, binary
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  19Q GAIN CNV         11    8
  19Q GAIN WILD-TYPE   61  100
        clus
vv       19Q GAIN CNV 19Q GAIN WILD-TYPE
  FEMALE           11                 61
  MALE              8                100
                    vv
clus                 STOMACH  ADENOCARCINOMA  DIFFUSE TYPE
  19Q GAIN CNV                                           1
  19Q GAIN WILD-TYPE                                     9
                    vv
clus                 STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  19Q GAIN CNV                                                            1
  19Q GAIN WILD-TYPE                                                     15
                    vv
clus                 STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  19Q GAIN CNV                                                                       1
  19Q GAIN WILD-TYPE                                                                 7
                    vv
clus                 STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE
  19Q GAIN CNV                                                              0
  19Q GAIN WILD-TYPE                                                        3
                    vv
clus                 STOMACH ADENOCARCINOMA  SIGNET RING TYPE
  19Q GAIN CNV                                              0
  19Q GAIN WILD-TYPE                                        1
                    vv
clus                 STOMACH ADENOCARCINOMA - DIFFUSE TYPE
  19Q GAIN CNV                                           3
  19Q GAIN WILD-TYPE                                    13
                    vv
clus                 STOMACH ADENOCARCINOMA - NOT OTHERWISE SPECIFIED (NOS)
  19Q GAIN CNV                                                            5
  19Q GAIN WILD-TYPE                                                     68
                    vv
clus                 STOMACH INTESTINAL ADENOCARCINOMA - MUCINOUS TYPE
  19Q GAIN CNV                                                       1
  19Q GAIN WILD-TYPE                                                 6
                    vv
clus                 STOMACH INTESTINAL ADENOCARCINOMA - PAPILLARY TYPE
  19Q GAIN CNV                                                        0
  19Q GAIN WILD-TYPE                                                  3
                    vv
clus                 STOMACH INTESTINAL ADENOCARCINOMA - TUBULAR TYPE
  19Q GAIN CNV                                                      2
  19Q GAIN WILD-TYPE                                                8
                    vv
clus                 STOMACH INTESTINAL ADENOCARCINOMA - TYPE NOT OTHERWISE SPECIFIED (NOS)
  19Q GAIN CNV                                                                            4
  19Q GAIN WILD-TYPE                                                                     24
D34V4, multiclass
                    vv
clus                 T1 T2 T3 T4
  19Q GAIN CNV        0  8  4  4
  19Q GAIN WILD-TYPE  6 44 52 14
D34V5, multiclass
    clus
vv   19Q GAIN CNV 19Q GAIN WILD-TYPE
  T1            0                  6
  T2            8                 44
  T3            4                 52
  T4            4                 14
                    vv
clus                 N0 N1 N2 N3
  19Q GAIN CNV        2  6  4  3
  19Q GAIN WILD-TYPE 42 43 19 12
D34V6, multiclass
    clus
vv   19Q GAIN CNV 19Q GAIN WILD-TYPE
  N0            2                 42
  N1            6                 43
  N2            4                 19
  N3            3                 12
                    vv
clus                  M0  M1  MX
  19Q GAIN CNV        12   4   0
  19Q GAIN WILD-TYPE 106  12   8
D34V7, multiclass
    clus
vv   19Q GAIN CNV 19Q GAIN WILD-TYPE
  M0           12                106
  M1            4                 12
  MX            0                  8
                    vv
clus                  I II III IV
  19Q GAIN CNV        2  2   3  8
  19Q GAIN WILD-TYPE 22 35  36 18
D34V8, multiclass
     clus
vv    19Q GAIN CNV 19Q GAIN WILD-TYPE
  I              2                 22
  II             2                 35
  III            3                 36
  IV             8                 18
D34V9, binary
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  19Q GAIN CNV          1   18
  19Q GAIN WILD-TYPE    4  157
     clus
vv    19Q GAIN CNV 19Q GAIN WILD-TYPE
  NO             1                  4
  YES           18                157
                    vv
clus                  R0  R1  R2  RX
  19Q GAIN CNV         9   2   4   2
  19Q GAIN WILD-TYPE 116   5   8  23
D34V10, multiclass
    clus
vv   19Q GAIN CNV 19Q GAIN WILD-TYPE
  R0            9                116
  R1            2                  5
  R2            4                  8
  RX            2                 23
D34V11, continuous

Clustering(35) Variable = 20p gain
D35V1, survival
                    sevent
clus2                 0  1
  20P GAIN CNV       54  6
  20P GAIN WILD-TYPE 70 13
      20P GAIN CNV 20P GAIN WILD-TYPE 
                60                 83 
      20P GAIN CNV 20P GAIN WILD-TYPE 
                 6                 13 
$`20P GAIN CNV`
TCGA-BR-6455 TCGA-BR-6458 TCGA-BR-6565 TCGA-BR-6706 TCGA-BR-6707 TCGA-BR-6801 
        1.41         1.35         0.62         2.17         0.99         1.12 
TCGA-BR-7197 TCGA-BR-7704 TCGA-BR-7715 TCGA-BR-7717 TCGA-BR-7722 TCGA-BR-7723 
        1.48         1.25         1.05         0.69         0.16         4.54 
TCGA-BR-7901 TCGA-BR-7958 TCGA-BR-7959 TCGA-BR-8060 TCGA-BR-8077 TCGA-BR-8295 
        0.95         0.16         1.08         1.32         0.69         1.55 
TCGA-BR-8296 TCGA-BR-A4J1 TCGA-BR-A4J4 TCGA-BR-A4J8 TCGA-BR-A4PF TCGA-BR-A4QI 
        1.48         0.72         0.53         0.23         0.72         0.49 
TCGA-CD-5799 TCGA-CD-5801 TCGA-CG-4300 TCGA-CG-4304 TCGA-CG-4305 TCGA-CG-4436 
        0.69         0.49        20.02        27.02        15.95        52.96 
TCGA-CG-4438 TCGA-CG-4440 TCGA-CG-4441 TCGA-CG-4444 TCGA-CG-4455 TCGA-CG-4466 
       54.05         4.01        14.01        47.05        12.03        18.94 
TCGA-CG-4469 TCGA-CG-5718 TCGA-CG-5726 TCGA-CG-5727 TCGA-CG-5730 TCGA-D7-5577 
        7.07         1.02        28.96        31.04         4.01         8.65 
TCGA-D7-5578 TCGA-D7-5579 TCGA-D7-6518 TCGA-D7-6521 TCGA-D7-6525 TCGA-D7-6528 
        3.58         4.54         9.80         8.19         5.95         1.68 
TCGA-D7-6818 TCGA-D7-6822 TCGA-EQ-8122 TCGA-F1-6874 TCGA-F1-6875 TCGA-FP-7829 
        4.04         4.27         7.79         2.01        72.23         0.20 
TCGA-FP-7916 TCGA-FP-7998 TCGA-FP-8099 TCGA-FP-8631 TCGA-IN-7806 TCGA-IN-7808 
        3.02         3.58         1.02         0.56         6.87         3.55 

$`20P GAIN WILD-TYPE`
TCGA-B7-5816 TCGA-B7-5818 TCGA-BR-6452 TCGA-BR-6457 TCGA-BR-6563 TCGA-BR-6564 
        5.62         0.10         0.95         1.35         0.85         0.82 
TCGA-BR-6566 TCGA-BR-6705 TCGA-BR-6709 TCGA-BR-6710 TCGA-BR-6802 TCGA-BR-6803 
        0.62         1.71         1.22         0.66         0.76         0.66 
TCGA-BR-6852 TCGA-BR-7196 TCGA-BR-7703 TCGA-BR-7707 TCGA-BR-7716 TCGA-BR-7851 
        0.26         1.22         0.46         0.13         0.82         0.99 
TCGA-BR-7957 TCGA-BR-8059 TCGA-BR-8078 TCGA-BR-8080 TCGA-BR-8081 TCGA-BR-8284 
        0.69         0.82         0.95         0.49         0.46         0.72 
TCGA-BR-8285 TCGA-BR-8286 TCGA-BR-8289 TCGA-BR-8291 TCGA-BR-8297 TCGA-BR-8592 
        0.26         0.43         0.26         1.18         0.76         0.20 
TCGA-BR-A4IU TCGA-BR-A4IV TCGA-BR-A4IY TCGA-BR-A4IZ TCGA-BR-A4J2 TCGA-BR-A4J5 
        0.59         0.92         0.39         0.79         0.79         0.43 
TCGA-BR-A4J6 TCGA-BR-A4J9 TCGA-BR-A4QL TCGA-CD-5798 TCGA-CD-5800 TCGA-CD-5802 
        0.13         0.10         2.24         0.82         0.36         0.30 
TCGA-CD-5803 TCGA-CG-4301 TCGA-CG-4306 TCGA-CG-4437 TCGA-CG-4443 TCGA-CG-4449 
        0.07         3.02         1.02         8.05        29.98        19.07 
TCGA-CG-4460 TCGA-CG-4462 TCGA-CG-4465 TCGA-CG-4472 TCGA-CG-4474 TCGA-CG-4477 
       21.99         1.02         8.98        12.00         1.02         1.02 
TCGA-CG-5716 TCGA-CG-5717 TCGA-CG-5719 TCGA-CG-5720 TCGA-CG-5721 TCGA-CG-5722 
        1.02         6.94         1.02         0.99         5.98         0.95 
TCGA-CG-5723 TCGA-CG-5724 TCGA-CG-5725 TCGA-CG-5728 TCGA-CG-5732 TCGA-CG-5733 
       70.06        12.03        15.02        65.10        55.04        21.07 
TCGA-CG-5734 TCGA-D7-6519 TCGA-D7-6520 TCGA-D7-6522 TCGA-D7-6524 TCGA-D7-6526 
        7.99        15.65         9.63         6.90         0.69         6.61 
TCGA-D7-6527 TCGA-D7-6815 TCGA-D7-6817 TCGA-D7-6820 TCGA-EQ-5647 TCGA-F1-6177 
        4.14         3.65         4.70         2.93         0.62         6.54 
TCGA-FP-7735 TCGA-FP-8209 TCGA-FP-8210 TCGA-HJ-7597 TCGA-IP-7968 
        0.39        59.05         5.03        26.43         2.53 

      20P GAIN CNV 20P GAIN WILD-TYPE 
              0.16               0.07 
      20P GAIN CNV 20P GAIN WILD-TYPE 
             72.23              70.06 
      20P GAIN CNV 20P GAIN WILD-TYPE 
              2.09               1.02 
[1] "0.2 - 72.2 (2.1)" "0.1 - 70.1 (1.0)"
        TCGA-B7-5816         TCGA-B7-5818         TCGA-BR-6452 
"20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE" 
        TCGA-BR-6455         TCGA-BR-6457         TCGA-BR-6458 
      "20P GAIN CNV" "20P GAIN WILD-TYPE"       "20P GAIN CNV" 
        TCGA-BR-6563         TCGA-BR-6564         TCGA-BR-6565 
"20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE"       "20P GAIN CNV" 
        TCGA-BR-6566         TCGA-BR-6705         TCGA-BR-6706 
"20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE"       "20P GAIN CNV" 
        TCGA-BR-6707         TCGA-BR-6709         TCGA-BR-6710 
      "20P GAIN CNV" "20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE" 
        TCGA-BR-6801         TCGA-BR-6802         TCGA-BR-6803 
      "20P GAIN CNV" "20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE" 
        TCGA-BR-6852         TCGA-BR-7196         TCGA-BR-7197 
"20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE"       "20P GAIN CNV" 
        TCGA-BR-7703         TCGA-BR-7704         TCGA-BR-7707 
"20P GAIN WILD-TYPE"       "20P GAIN CNV" "20P GAIN WILD-TYPE" 
        TCGA-BR-7715         TCGA-BR-7716         TCGA-BR-7717 
      "20P GAIN CNV" "20P GAIN WILD-TYPE"       "20P GAIN CNV" 
        TCGA-BR-7722         TCGA-BR-7723         TCGA-BR-7851 
      "20P GAIN CNV"       "20P GAIN CNV" "20P GAIN WILD-TYPE" 
        TCGA-BR-7901         TCGA-BR-7957         TCGA-BR-7958 
      "20P GAIN CNV" "20P GAIN WILD-TYPE"       "20P GAIN CNV" 
        TCGA-BR-7959         TCGA-BR-8059         TCGA-BR-8060 
      "20P GAIN CNV" "20P GAIN WILD-TYPE"       "20P GAIN CNV" 
        TCGA-BR-8077         TCGA-BR-8078         TCGA-BR-8080 
      "20P GAIN CNV" "20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE" 
        TCGA-BR-8081         TCGA-BR-8284         TCGA-BR-8285 
"20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE" 
        TCGA-BR-8286         TCGA-BR-8289         TCGA-BR-8291 
"20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE" 
        TCGA-BR-8295         TCGA-BR-8296         TCGA-BR-8297 
      "20P GAIN CNV"       "20P GAIN CNV" "20P GAIN WILD-TYPE" 
        TCGA-BR-8592         TCGA-BR-A4IU         TCGA-BR-A4IV 
"20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE" 
        TCGA-BR-A4IY         TCGA-BR-A4IZ         TCGA-BR-A4J1 
"20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE"       "20P GAIN CNV" 
        TCGA-BR-A4J2         TCGA-BR-A4J4         TCGA-BR-A4J5 
"20P GAIN WILD-TYPE"       "20P GAIN CNV" "20P GAIN WILD-TYPE" 
        TCGA-BR-A4J6         TCGA-BR-A4J8         TCGA-BR-A4J9 
"20P GAIN WILD-TYPE"       "20P GAIN CNV" "20P GAIN WILD-TYPE" 
        TCGA-BR-A4PF         TCGA-BR-A4QI         TCGA-BR-A4QL 
      "20P GAIN CNV"       "20P GAIN CNV" "20P GAIN WILD-TYPE" 
        TCGA-CD-5798         TCGA-CD-5799         TCGA-CD-5800 
"20P GAIN WILD-TYPE"       "20P GAIN CNV" "20P GAIN WILD-TYPE" 
        TCGA-CD-5801         TCGA-CD-5802         TCGA-CD-5803 
      "20P GAIN CNV" "20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE" 
        TCGA-CG-4300         TCGA-CG-4301         TCGA-CG-4304 
      "20P GAIN CNV" "20P GAIN WILD-TYPE"       "20P GAIN CNV" 
        TCGA-CG-4305         TCGA-CG-4306         TCGA-CG-4436 
      "20P GAIN CNV" "20P GAIN WILD-TYPE"       "20P GAIN CNV" 
        TCGA-CG-4437         TCGA-CG-4438         TCGA-CG-4440 
"20P GAIN WILD-TYPE"       "20P GAIN CNV"       "20P GAIN CNV" 
        TCGA-CG-4441         TCGA-CG-4443         TCGA-CG-4444 
      "20P GAIN CNV" "20P GAIN WILD-TYPE"       "20P GAIN CNV" 
        TCGA-CG-4449         TCGA-CG-4455         TCGA-CG-4460 
"20P GAIN WILD-TYPE"       "20P GAIN CNV" "20P GAIN WILD-TYPE" 
        TCGA-CG-4462         TCGA-CG-4465         TCGA-CG-4466 
"20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE"       "20P GAIN CNV" 
        TCGA-CG-4469         TCGA-CG-4472         TCGA-CG-4474 
      "20P GAIN CNV" "20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE" 
        TCGA-CG-4477         TCGA-CG-5716         TCGA-CG-5717 
"20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE" 
        TCGA-CG-5718         TCGA-CG-5719         TCGA-CG-5720 
      "20P GAIN CNV" "20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE" 
        TCGA-CG-5721         TCGA-CG-5722         TCGA-CG-5723 
"20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE" 
        TCGA-CG-5724         TCGA-CG-5725         TCGA-CG-5726 
"20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE"       "20P GAIN CNV" 
        TCGA-CG-5727         TCGA-CG-5728         TCGA-CG-5730 
      "20P GAIN CNV" "20P GAIN WILD-TYPE"       "20P GAIN CNV" 
        TCGA-CG-5732         TCGA-CG-5733         TCGA-CG-5734 
"20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE" 
        TCGA-D7-5577         TCGA-D7-5578         TCGA-D7-5579 
      "20P GAIN CNV"       "20P GAIN CNV"       "20P GAIN CNV" 
        TCGA-D7-6518         TCGA-D7-6519         TCGA-D7-6520 
      "20P GAIN CNV" "20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE" 
        TCGA-D7-6521         TCGA-D7-6522         TCGA-D7-6524 
      "20P GAIN CNV" "20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE" 
        TCGA-D7-6525         TCGA-D7-6526         TCGA-D7-6527 
      "20P GAIN CNV" "20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE" 
        TCGA-D7-6528         TCGA-D7-6815         TCGA-D7-6817 
      "20P GAIN CNV" "20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE" 
        TCGA-D7-6818         TCGA-D7-6820         TCGA-D7-6822 
      "20P GAIN CNV" "20P GAIN WILD-TYPE"       "20P GAIN CNV" 
        TCGA-EQ-5647         TCGA-EQ-8122         TCGA-F1-6177 
"20P GAIN WILD-TYPE"       "20P GAIN CNV" "20P GAIN WILD-TYPE" 
        TCGA-F1-6874         TCGA-F1-6875         TCGA-FP-7735 
      "20P GAIN CNV"       "20P GAIN CNV" "20P GAIN WILD-TYPE" 
        TCGA-FP-7829         TCGA-FP-7916         TCGA-FP-7998 
      "20P GAIN CNV"       "20P GAIN CNV"       "20P GAIN CNV" 
        TCGA-FP-8099         TCGA-FP-8209         TCGA-FP-8210 
      "20P GAIN CNV" "20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE" 
        TCGA-FP-8631         TCGA-HJ-7597         TCGA-IN-7806 
      "20P GAIN CNV" "20P GAIN WILD-TYPE"       "20P GAIN CNV" 
        TCGA-IN-7808         TCGA-IP-7968 
      "20P GAIN CNV" "20P GAIN WILD-TYPE" 
        TCGA-B7-5816         TCGA-B7-5818         TCGA-BR-6452 
"20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE" 
        TCGA-BR-6455         TCGA-BR-6457         TCGA-BR-6458 
      "20P GAIN CNV" "20P GAIN WILD-TYPE"       "20P GAIN CNV" 
        TCGA-BR-6563         TCGA-BR-6564         TCGA-BR-6565 
"20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE"       "20P GAIN CNV" 
        TCGA-BR-6566         TCGA-BR-6705         TCGA-BR-6706 
"20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE"       "20P GAIN CNV" 
        TCGA-BR-6707         TCGA-BR-6709         TCGA-BR-6710 
      "20P GAIN CNV" "20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE" 
        TCGA-BR-6801         TCGA-BR-6802         TCGA-BR-6803 
      "20P GAIN CNV" "20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE" 
        TCGA-BR-6852         TCGA-BR-7196         TCGA-BR-7197 
"20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE"       "20P GAIN CNV" 
        TCGA-BR-7703         TCGA-BR-7704         TCGA-BR-7707 
"20P GAIN WILD-TYPE"       "20P GAIN CNV" "20P GAIN WILD-TYPE" 
        TCGA-BR-7715         TCGA-BR-7716         TCGA-BR-7717 
      "20P GAIN CNV" "20P GAIN WILD-TYPE"       "20P GAIN CNV" 
        TCGA-BR-7722         TCGA-BR-7723         TCGA-BR-7851 
      "20P GAIN CNV"       "20P GAIN CNV" "20P GAIN WILD-TYPE" 
        TCGA-BR-7901         TCGA-BR-7957         TCGA-BR-7958 
      "20P GAIN CNV" "20P GAIN WILD-TYPE"       "20P GAIN CNV" 
        TCGA-BR-7959         TCGA-BR-8059         TCGA-BR-8060 
      "20P GAIN CNV" "20P GAIN WILD-TYPE"       "20P GAIN CNV" 
        TCGA-BR-8077         TCGA-BR-8078         TCGA-BR-8080 
      "20P GAIN CNV" "20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE" 
        TCGA-BR-8081         TCGA-BR-8284         TCGA-BR-8285 
"20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE" 
        TCGA-BR-8286         TCGA-BR-8289         TCGA-BR-8291 
"20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE" 
        TCGA-BR-8295         TCGA-BR-8296         TCGA-BR-8297 
      "20P GAIN CNV"       "20P GAIN CNV" "20P GAIN WILD-TYPE" 
        TCGA-BR-8592         TCGA-BR-A4IU         TCGA-BR-A4IV 
"20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE" 
        TCGA-BR-A4IY         TCGA-BR-A4IZ         TCGA-BR-A4J1 
"20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE"       "20P GAIN CNV" 
        TCGA-BR-A4J2         TCGA-BR-A4J4         TCGA-BR-A4J5 
"20P GAIN WILD-TYPE"       "20P GAIN CNV" "20P GAIN WILD-TYPE" 
        TCGA-BR-A4J6         TCGA-BR-A4J8         TCGA-BR-A4J9 
"20P GAIN WILD-TYPE"       "20P GAIN CNV" "20P GAIN WILD-TYPE" 
        TCGA-BR-A4PF         TCGA-BR-A4QI         TCGA-BR-A4QL 
      "20P GAIN CNV"       "20P GAIN CNV" "20P GAIN WILD-TYPE" 
        TCGA-CD-5798         TCGA-CD-5799         TCGA-CD-5800 
"20P GAIN WILD-TYPE"       "20P GAIN CNV" "20P GAIN WILD-TYPE" 
        TCGA-CD-5801         TCGA-CD-5802         TCGA-CD-5803 
      "20P GAIN CNV" "20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE" 
        TCGA-CG-4300         TCGA-CG-4301         TCGA-CG-4304 
      "20P GAIN CNV" "20P GAIN WILD-TYPE"       "20P GAIN CNV" 
        TCGA-CG-4305         TCGA-CG-4306         TCGA-CG-4436 
      "20P GAIN CNV" "20P GAIN WILD-TYPE"       "20P GAIN CNV" 
        TCGA-CG-4437         TCGA-CG-4438         TCGA-CG-4440 
"20P GAIN WILD-TYPE"       "20P GAIN CNV"       "20P GAIN CNV" 
        TCGA-CG-4441         TCGA-CG-4443         TCGA-CG-4444 
      "20P GAIN CNV" "20P GAIN WILD-TYPE"       "20P GAIN CNV" 
        TCGA-CG-4449         TCGA-CG-4455         TCGA-CG-4460 
"20P GAIN WILD-TYPE"       "20P GAIN CNV" "20P GAIN WILD-TYPE" 
        TCGA-CG-4462         TCGA-CG-4465         TCGA-CG-4466 
"20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE"       "20P GAIN CNV" 
        TCGA-CG-4469         TCGA-CG-4472         TCGA-CG-4474 
      "20P GAIN CNV" "20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE" 
        TCGA-CG-4477         TCGA-CG-5716         TCGA-CG-5717 
"20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE" 
        TCGA-CG-5718         TCGA-CG-5719         TCGA-CG-5720 
      "20P GAIN CNV" "20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE" 
        TCGA-CG-5721         TCGA-CG-5722         TCGA-CG-5723 
"20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE" 
        TCGA-CG-5724         TCGA-CG-5725         TCGA-CG-5726 
"20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE"       "20P GAIN CNV" 
        TCGA-CG-5727         TCGA-CG-5728         TCGA-CG-5730 
      "20P GAIN CNV" "20P GAIN WILD-TYPE"       "20P GAIN CNV" 
        TCGA-CG-5732         TCGA-CG-5733         TCGA-CG-5734 
"20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE" 
        TCGA-D7-5577         TCGA-D7-5578         TCGA-D7-5579 
      "20P GAIN CNV"       "20P GAIN CNV"       "20P GAIN CNV" 
        TCGA-D7-6518         TCGA-D7-6519         TCGA-D7-6520 
      "20P GAIN CNV" "20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE" 
        TCGA-D7-6521         TCGA-D7-6522         TCGA-D7-6524 
      "20P GAIN CNV" "20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE" 
        TCGA-D7-6525         TCGA-D7-6526         TCGA-D7-6527 
      "20P GAIN CNV" "20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE" 
        TCGA-D7-6528         TCGA-D7-6815         TCGA-D7-6817 
      "20P GAIN CNV" "20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE" 
        TCGA-D7-6818         TCGA-D7-6820         TCGA-D7-6822 
      "20P GAIN CNV" "20P GAIN WILD-TYPE"       "20P GAIN CNV" 
        TCGA-EQ-5647         TCGA-EQ-8122         TCGA-F1-6177 
"20P GAIN WILD-TYPE"       "20P GAIN CNV" "20P GAIN WILD-TYPE" 
        TCGA-F1-6874         TCGA-F1-6875         TCGA-FP-7735 
      "20P GAIN CNV"       "20P GAIN CNV" "20P GAIN WILD-TYPE" 
        TCGA-FP-7829         TCGA-FP-7916         TCGA-FP-7998 
      "20P GAIN CNV"       "20P GAIN CNV"       "20P GAIN CNV" 
        TCGA-FP-8099         TCGA-FP-8209         TCGA-FP-8210 
      "20P GAIN CNV" "20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE" 
        TCGA-FP-8631         TCGA-HJ-7597         TCGA-IN-7806 
      "20P GAIN CNV" "20P GAIN WILD-TYPE"       "20P GAIN CNV" 
        TCGA-IN-7808         TCGA-IP-7968 
      "20P GAIN CNV" "20P GAIN WILD-TYPE" 
        TCGA-B7-5816         TCGA-B7-5818         TCGA-BR-6452 
"20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE" 
        TCGA-BR-6455         TCGA-BR-6457         TCGA-BR-6458 
      "20P GAIN CNV" "20P GAIN WILD-TYPE"       "20P GAIN CNV" 
        TCGA-BR-6563         TCGA-BR-6564         TCGA-BR-6565 
"20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE"       "20P GAIN CNV" 
        TCGA-BR-6566         TCGA-BR-6705         TCGA-BR-6706 
"20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE"       "20P GAIN CNV" 
        TCGA-BR-6707         TCGA-BR-6709         TCGA-BR-6710 
      "20P GAIN CNV" "20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE" 
        TCGA-BR-6801         TCGA-BR-6802         TCGA-BR-6803 
      "20P GAIN CNV" "20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE" 
        TCGA-BR-6852         TCGA-BR-7196         TCGA-BR-7197 
"20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE"       "20P GAIN CNV" 
        TCGA-BR-7703         TCGA-BR-7704         TCGA-BR-7707 
"20P GAIN WILD-TYPE"       "20P GAIN CNV" "20P GAIN WILD-TYPE" 
        TCGA-BR-7715         TCGA-BR-7716         TCGA-BR-7717 
      "20P GAIN CNV" "20P GAIN WILD-TYPE"       "20P GAIN CNV" 
        TCGA-BR-7722         TCGA-BR-7723         TCGA-BR-7851 
      "20P GAIN CNV"       "20P GAIN CNV" "20P GAIN WILD-TYPE" 
        TCGA-BR-7901         TCGA-BR-7957         TCGA-BR-7958 
      "20P GAIN CNV" "20P GAIN WILD-TYPE"       "20P GAIN CNV" 
        TCGA-BR-7959         TCGA-BR-8059         TCGA-BR-8060 
      "20P GAIN CNV" "20P GAIN WILD-TYPE"       "20P GAIN CNV" 
        TCGA-BR-8077         TCGA-BR-8078         TCGA-BR-8080 
      "20P GAIN CNV" "20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE" 
        TCGA-BR-8081         TCGA-BR-8284         TCGA-BR-8285 
"20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE" 
        TCGA-BR-8286         TCGA-BR-8289         TCGA-BR-8291 
"20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE" 
        TCGA-BR-8295         TCGA-BR-8296         TCGA-BR-8297 
      "20P GAIN CNV"       "20P GAIN CNV" "20P GAIN WILD-TYPE" 
        TCGA-BR-8592         TCGA-BR-A4IU         TCGA-BR-A4IV 
"20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE" 
        TCGA-BR-A4IY         TCGA-BR-A4IZ         TCGA-BR-A4J1 
"20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE"       "20P GAIN CNV" 
        TCGA-BR-A4J2         TCGA-BR-A4J4         TCGA-BR-A4J5 
"20P GAIN WILD-TYPE"       "20P GAIN CNV" "20P GAIN WILD-TYPE" 
        TCGA-BR-A4J6         TCGA-BR-A4J8         TCGA-BR-A4J9 
"20P GAIN WILD-TYPE"       "20P GAIN CNV" "20P GAIN WILD-TYPE" 
        TCGA-BR-A4PF         TCGA-BR-A4QI         TCGA-BR-A4QL 
      "20P GAIN CNV"       "20P GAIN CNV" "20P GAIN WILD-TYPE" 
        TCGA-CD-5798         TCGA-CD-5799         TCGA-CD-5800 
"20P GAIN WILD-TYPE"       "20P GAIN CNV" "20P GAIN WILD-TYPE" 
        TCGA-CD-5801         TCGA-CD-5802         TCGA-CD-5803 
      "20P GAIN CNV" "20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE" 
        TCGA-CG-4300         TCGA-CG-4301         TCGA-CG-4304 
      "20P GAIN CNV" "20P GAIN WILD-TYPE"       "20P GAIN CNV" 
        TCGA-CG-4305         TCGA-CG-4306         TCGA-CG-4436 
      "20P GAIN CNV" "20P GAIN WILD-TYPE"       "20P GAIN CNV" 
        TCGA-CG-4437         TCGA-CG-4438         TCGA-CG-4440 
"20P GAIN WILD-TYPE"       "20P GAIN CNV"       "20P GAIN CNV" 
        TCGA-CG-4441         TCGA-CG-4443         TCGA-CG-4444 
      "20P GAIN CNV" "20P GAIN WILD-TYPE"       "20P GAIN CNV" 
        TCGA-CG-4449         TCGA-CG-4455         TCGA-CG-4460 
"20P GAIN WILD-TYPE"       "20P GAIN CNV" "20P GAIN WILD-TYPE" 
        TCGA-CG-4462         TCGA-CG-4465         TCGA-CG-4466 
"20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE"       "20P GAIN CNV" 
        TCGA-CG-4469         TCGA-CG-4472         TCGA-CG-4474 
      "20P GAIN CNV" "20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE" 
        TCGA-CG-4477         TCGA-CG-5716         TCGA-CG-5717 
"20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE" 
        TCGA-CG-5718         TCGA-CG-5719         TCGA-CG-5720 
      "20P GAIN CNV" "20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE" 
        TCGA-CG-5721         TCGA-CG-5722         TCGA-CG-5723 
"20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE" 
        TCGA-CG-5724         TCGA-CG-5725         TCGA-CG-5726 
"20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE"       "20P GAIN CNV" 
        TCGA-CG-5727         TCGA-CG-5728         TCGA-CG-5730 
      "20P GAIN CNV" "20P GAIN WILD-TYPE"       "20P GAIN CNV" 
        TCGA-CG-5732         TCGA-CG-5733         TCGA-CG-5734 
"20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE" 
        TCGA-D7-5577         TCGA-D7-5578         TCGA-D7-5579 
      "20P GAIN CNV"       "20P GAIN CNV"       "20P GAIN CNV" 
        TCGA-D7-6518         TCGA-D7-6519         TCGA-D7-6520 
      "20P GAIN CNV" "20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE" 
        TCGA-D7-6521         TCGA-D7-6522         TCGA-D7-6524 
      "20P GAIN CNV" "20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE" 
        TCGA-D7-6525         TCGA-D7-6526         TCGA-D7-6527 
      "20P GAIN CNV" "20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE" 
        TCGA-D7-6528         TCGA-D7-6815         TCGA-D7-6817 
      "20P GAIN CNV" "20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE" 
        TCGA-D7-6818         TCGA-D7-6820         TCGA-D7-6822 
      "20P GAIN CNV" "20P GAIN WILD-TYPE"       "20P GAIN CNV" 
        TCGA-EQ-5647         TCGA-EQ-8122         TCGA-F1-6177 
"20P GAIN WILD-TYPE"       "20P GAIN CNV" "20P GAIN WILD-TYPE" 
        TCGA-F1-6874         TCGA-F1-6875         TCGA-FP-7735 
      "20P GAIN CNV"       "20P GAIN CNV" "20P GAIN WILD-TYPE" 
        TCGA-FP-7829         TCGA-FP-7916         TCGA-FP-7998 
      "20P GAIN CNV"       "20P GAIN CNV"       "20P GAIN CNV" 
        TCGA-FP-8099         TCGA-FP-8209         TCGA-FP-8210 
      "20P GAIN CNV" "20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE" 
        TCGA-FP-8631         TCGA-HJ-7597         TCGA-IN-7806 
      "20P GAIN CNV" "20P GAIN WILD-TYPE"       "20P GAIN CNV" 
        TCGA-IN-7808         TCGA-IP-7968 
      "20P GAIN CNV" "20P GAIN WILD-TYPE" 
[1] "hr=" "2.4"
D35V2, continuous
D35V3, binary
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  20P GAIN CNV         20   54
  20P GAIN WILD-TYPE   52   54
        clus
vv       20P GAIN CNV 20P GAIN WILD-TYPE
  FEMALE           20                 52
  MALE             54                 54
                    vv
clus                 STOMACH  ADENOCARCINOMA  DIFFUSE TYPE
  20P GAIN CNV                                           1
  20P GAIN WILD-TYPE                                     9
                    vv
clus                 STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  20P GAIN CNV                                                            9
  20P GAIN WILD-TYPE                                                      7
                    vv
clus                 STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  20P GAIN CNV                                                                       4
  20P GAIN WILD-TYPE                                                                 4
                    vv
clus                 STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE
  20P GAIN CNV                                                              1
  20P GAIN WILD-TYPE                                                        2
                    vv
clus                 STOMACH ADENOCARCINOMA  SIGNET RING TYPE
  20P GAIN CNV                                              0
  20P GAIN WILD-TYPE                                        1
                    vv
clus                 STOMACH ADENOCARCINOMA - DIFFUSE TYPE
  20P GAIN CNV                                           8
  20P GAIN WILD-TYPE                                     8
                    vv
clus                 STOMACH ADENOCARCINOMA - NOT OTHERWISE SPECIFIED (NOS)
  20P GAIN CNV                                                           29
  20P GAIN WILD-TYPE                                                     44
                    vv
clus                 STOMACH INTESTINAL ADENOCARCINOMA - MUCINOUS TYPE
  20P GAIN CNV                                                       3
  20P GAIN WILD-TYPE                                                 4
                    vv
clus                 STOMACH INTESTINAL ADENOCARCINOMA - PAPILLARY TYPE
  20P GAIN CNV                                                        0
  20P GAIN WILD-TYPE                                                  3
                    vv
clus                 STOMACH INTESTINAL ADENOCARCINOMA - TUBULAR TYPE
  20P GAIN CNV                                                      5
  20P GAIN WILD-TYPE                                                5
                    vv
clus                 STOMACH INTESTINAL ADENOCARCINOMA - TYPE NOT OTHERWISE SPECIFIED (NOS)
  20P GAIN CNV                                                                           13
  20P GAIN WILD-TYPE                                                                     15
D35V4, multiclass
                    vv
clus                 T1 T2 T3 T4
  20P GAIN CNV        1 23 26  5
  20P GAIN WILD-TYPE  5 29 30 13
D35V5, multiclass
    clus
vv   20P GAIN CNV 20P GAIN WILD-TYPE
  T1            1                  5
  T2           23                 29
  T3           26                 30
  T4            5                 13
                    vv
clus                 N0 N1 N2 N3
  20P GAIN CNV       15 21  9  8
  20P GAIN WILD-TYPE 29 28 14  7
D35V6, multiclass
    clus
vv   20P GAIN CNV 20P GAIN WILD-TYPE
  N0           15                 29
  N1           21                 28
  N2            9                 14
  N3            8                  7
                    vv
clus                 M0 M1 MX
  20P GAIN CNV       53  3  3
  20P GAIN WILD-TYPE 65 13  5
D35V7, multiclass
    clus
vv   20P GAIN CNV 20P GAIN WILD-TYPE
  M0           53                 65
  M1            3                 13
  MX            3                  5
                    vv
clus                  I II III IV
  20P GAIN CNV        8 14  22  7
  20P GAIN WILD-TYPE 16 23  17 19
D35V8, multiclass
     clus
vv    20P GAIN CNV 20P GAIN WILD-TYPE
  I              8                 16
  II            14                 23
  III           22                 17
  IV             7                 19
D35V9, binary
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  20P GAIN CNV          1   73
  20P GAIN WILD-TYPE    4  102
     clus
vv    20P GAIN CNV 20P GAIN WILD-TYPE
  NO             1                  4
  YES           73                102
                    vv
clus                 R0 R1 R2 RX
  20P GAIN CNV       51  4  2 12
  20P GAIN WILD-TYPE 74  3 10 13
D35V10, multiclass
    clus
vv   20P GAIN CNV 20P GAIN WILD-TYPE
  R0           51                 74
  R1            4                  3
  R2            2                 10
  RX           12                 13
D35V11, continuous

Clustering(36) Variable = 20q gain
D36V1, survival
                    sevent
clus2                 0  1
  20Q GAIN CNV       63  7
  20Q GAIN WILD-TYPE 61 12
      20Q GAIN CNV 20Q GAIN WILD-TYPE 
                70                 73 
      20Q GAIN CNV 20Q GAIN WILD-TYPE 
                 7                 12 
$`20Q GAIN CNV`
TCGA-BR-6455 TCGA-BR-6458 TCGA-BR-6565 TCGA-BR-6706 TCGA-BR-6707 TCGA-BR-6801 
        1.41         1.35         0.62         2.17         0.99         1.12 
TCGA-BR-7197 TCGA-BR-7704 TCGA-BR-7715 TCGA-BR-7717 TCGA-BR-7722 TCGA-BR-7723 
        1.48         1.25         1.05         0.69         0.16         4.54 
TCGA-BR-7901 TCGA-BR-7958 TCGA-BR-7959 TCGA-BR-8059 TCGA-BR-8060 TCGA-BR-8077 
        0.95         0.16         1.08         0.82         1.32         0.69 
TCGA-BR-8289 TCGA-BR-8295 TCGA-BR-8296 TCGA-BR-A4J1 TCGA-BR-A4J4 TCGA-BR-A4J8 
        0.26         1.55         1.48         0.72         0.53         0.23 
TCGA-BR-A4PF TCGA-BR-A4QI TCGA-CD-5799 TCGA-CD-5800 TCGA-CD-5801 TCGA-CG-4300 
        0.72         0.49         0.69         0.36         0.49        20.02 
TCGA-CG-4304 TCGA-CG-4305 TCGA-CG-4436 TCGA-CG-4438 TCGA-CG-4440 TCGA-CG-4441 
       27.02        15.95        52.96        54.05         4.01        14.01 
TCGA-CG-4444 TCGA-CG-4455 TCGA-CG-4466 TCGA-CG-4469 TCGA-CG-5718 TCGA-CG-5724 
       47.05        12.03        18.94         7.07         1.02        12.03 
TCGA-CG-5726 TCGA-CG-5727 TCGA-CG-5730 TCGA-CG-5732 TCGA-D7-5577 TCGA-D7-5578 
       28.96        31.04         4.01        55.04         8.65         3.58 
TCGA-D7-5579 TCGA-D7-6518 TCGA-D7-6520 TCGA-D7-6521 TCGA-D7-6525 TCGA-D7-6526 
        4.54         9.80         9.63         8.19         5.95         6.61 
TCGA-D7-6528 TCGA-D7-6815 TCGA-D7-6818 TCGA-D7-6822 TCGA-EQ-8122 TCGA-F1-6874 
        1.68         3.65         4.04         4.27         7.79         2.01 
TCGA-F1-6875 TCGA-FP-7735 TCGA-FP-7829 TCGA-FP-7916 TCGA-FP-7998 TCGA-FP-8099 
       72.23         0.39         0.20         3.02         3.58         1.02 
TCGA-FP-8631 TCGA-IN-7806 TCGA-IN-7808 TCGA-IP-7968 
        0.56         6.87         3.55         2.53 

$`20Q GAIN WILD-TYPE`
TCGA-B7-5816 TCGA-B7-5818 TCGA-BR-6452 TCGA-BR-6457 TCGA-BR-6563 TCGA-BR-6564 
        5.62         0.10         0.95         1.35         0.85         0.82 
TCGA-BR-6566 TCGA-BR-6705 TCGA-BR-6709 TCGA-BR-6710 TCGA-BR-6802 TCGA-BR-6803 
        0.62         1.71         1.22         0.66         0.76         0.66 
TCGA-BR-6852 TCGA-BR-7196 TCGA-BR-7703 TCGA-BR-7707 TCGA-BR-7716 TCGA-BR-7851 
        0.26         1.22         0.46         0.13         0.82         0.99 
TCGA-BR-7957 TCGA-BR-8078 TCGA-BR-8080 TCGA-BR-8081 TCGA-BR-8284 TCGA-BR-8285 
        0.69         0.95         0.49         0.46         0.72         0.26 
TCGA-BR-8286 TCGA-BR-8291 TCGA-BR-8297 TCGA-BR-8592 TCGA-BR-A4IU TCGA-BR-A4IV 
        0.43         1.18         0.76         0.20         0.59         0.92 
TCGA-BR-A4IY TCGA-BR-A4IZ TCGA-BR-A4J2 TCGA-BR-A4J5 TCGA-BR-A4J6 TCGA-BR-A4J9 
        0.39         0.79         0.79         0.43         0.13         0.10 
TCGA-BR-A4QL TCGA-CD-5798 TCGA-CD-5802 TCGA-CD-5803 TCGA-CG-4301 TCGA-CG-4306 
        2.24         0.82         0.30         0.07         3.02         1.02 
TCGA-CG-4437 TCGA-CG-4443 TCGA-CG-4449 TCGA-CG-4460 TCGA-CG-4462 TCGA-CG-4465 
        8.05        29.98        19.07        21.99         1.02         8.98 
TCGA-CG-4472 TCGA-CG-4474 TCGA-CG-4477 TCGA-CG-5716 TCGA-CG-5717 TCGA-CG-5719 
       12.00         1.02         1.02         1.02         6.94         1.02 
TCGA-CG-5720 TCGA-CG-5721 TCGA-CG-5722 TCGA-CG-5723 TCGA-CG-5725 TCGA-CG-5728 
        0.99         5.98         0.95        70.06        15.02        65.10 
TCGA-CG-5733 TCGA-CG-5734 TCGA-D7-6519 TCGA-D7-6522 TCGA-D7-6524 TCGA-D7-6527 
       21.07         7.99        15.65         6.90         0.69         4.14 
TCGA-D7-6817 TCGA-D7-6820 TCGA-EQ-5647 TCGA-F1-6177 TCGA-FP-8209 TCGA-FP-8210 
        4.70         2.93         0.62         6.54        59.05         5.03 
TCGA-HJ-7597 
       26.43 

      20Q GAIN CNV 20Q GAIN WILD-TYPE 
              0.16               0.07 
      20Q GAIN CNV 20Q GAIN WILD-TYPE 
             72.23              70.06 
      20Q GAIN CNV 20Q GAIN WILD-TYPE 
              2.35               0.99 
[1] "0.2 - 72.2 (2.3)" "0.1 - 70.1 (1.0)"
        TCGA-B7-5816         TCGA-B7-5818         TCGA-BR-6452 
"20Q GAIN WILD-TYPE" "20Q GAIN WILD-TYPE" "20Q GAIN WILD-TYPE" 
        TCGA-BR-6455         TCGA-BR-6457         TCGA-BR-6458 
      "20Q GAIN CNV" "20Q GAIN WILD-TYPE"       "20Q GAIN CNV" 
        TCGA-BR-6563         TCGA-BR-6564         TCGA-BR-6565 
"20Q GAIN WILD-TYPE" "20Q GAIN WILD-TYPE"       "20Q GAIN CNV" 
        TCGA-BR-6566         TCGA-BR-6705         TCGA-BR-6706 
"20Q GAIN WILD-TYPE" "20Q GAIN WILD-TYPE"       "20Q GAIN CNV" 
        TCGA-BR-6707         TCGA-BR-6709         TCGA-BR-6710 
      "20Q GAIN CNV" "20Q GAIN WILD-TYPE" "20Q GAIN WILD-TYPE" 
        TCGA-BR-6801         TCGA-BR-6802         TCGA-BR-6803 
      "20Q GAIN CNV" "20Q GAIN WILD-TYPE" "20Q GAIN WILD-TYPE" 
        TCGA-BR-6852         TCGA-BR-7196         TCGA-BR-7197 
"20Q GAIN WILD-TYPE" "20Q GAIN WILD-TYPE"       "20Q GAIN CNV" 
        TCGA-BR-7703         TCGA-BR-7704         TCGA-BR-7707 
"20Q GAIN WILD-TYPE"       "20Q GAIN CNV" "20Q GAIN WILD-TYPE" 
        TCGA-BR-7715         TCGA-BR-7716         TCGA-BR-7717 
      "20Q GAIN CNV" "20Q GAIN WILD-TYPE"       "20Q GAIN CNV" 
        TCGA-BR-7722         TCGA-BR-7723         TCGA-BR-7851 
      "20Q GAIN CNV"       "20Q GAIN CNV" "20Q GAIN WILD-TYPE" 
        TCGA-BR-7901         TCGA-BR-7957         TCGA-BR-7958 
      "20Q GAIN CNV" "20Q GAIN WILD-TYPE"       "20Q GAIN CNV" 
        TCGA-BR-7959         TCGA-BR-8059         TCGA-BR-8060 
      "20Q GAIN CNV"       "20Q GAIN CNV"       "20Q GAIN CNV" 
        TCGA-BR-8077         TCGA-BR-8078         TCGA-BR-8080 
      "20Q GAIN CNV" "20Q GAIN WILD-TYPE" "20Q GAIN WILD-TYPE" 
        TCGA-BR-8081         TCGA-BR-8284         TCGA-BR-8285 
"20Q GAIN WILD-TYPE" "20Q GAIN WILD-TYPE" "20Q GAIN WILD-TYPE" 
        TCGA-BR-8286         TCGA-BR-8289         TCGA-BR-8291 
"20Q GAIN WILD-TYPE"       "20Q GAIN CNV" "20Q GAIN WILD-TYPE" 
        TCGA-BR-8295         TCGA-BR-8296         TCGA-BR-8297 
      "20Q GAIN CNV"       "20Q GAIN CNV" "20Q GAIN WILD-TYPE" 
        TCGA-BR-8592         TCGA-BR-A4IU         TCGA-BR-A4IV 
"20Q GAIN WILD-TYPE" "20Q GAIN WILD-TYPE" "20Q GAIN WILD-TYPE" 
        TCGA-BR-A4IY         TCGA-BR-A4IZ         TCGA-BR-A4J1 
"20Q GAIN WILD-TYPE" "20Q GAIN WILD-TYPE"       "20Q GAIN CNV" 
        TCGA-BR-A4J2         TCGA-BR-A4J4         TCGA-BR-A4J5 
"20Q GAIN WILD-TYPE"       "20Q GAIN CNV" "20Q GAIN WILD-TYPE" 
        TCGA-BR-A4J6         TCGA-BR-A4J8         TCGA-BR-A4J9 
"20Q GAIN WILD-TYPE"       "20Q GAIN CNV" "20Q GAIN WILD-TYPE" 
        TCGA-BR-A4PF         TCGA-BR-A4QI         TCGA-BR-A4QL 
      "20Q GAIN CNV"       "20Q GAIN CNV" "20Q GAIN WILD-TYPE" 
        TCGA-CD-5798         TCGA-CD-5799         TCGA-CD-5800 
"20Q GAIN WILD-TYPE"       "20Q GAIN CNV"       "20Q GAIN CNV" 
        TCGA-CD-5801         TCGA-CD-5802         TCGA-CD-5803 
      "20Q GAIN CNV" "20Q GAIN WILD-TYPE" "20Q GAIN WILD-TYPE" 
        TCGA-CG-4300         TCGA-CG-4301         TCGA-CG-4304 
      "20Q GAIN CNV" "20Q GAIN WILD-TYPE"       "20Q GAIN CNV" 
        TCGA-CG-4305         TCGA-CG-4306         TCGA-CG-4436 
      "20Q GAIN CNV" "20Q GAIN WILD-TYPE"       "20Q GAIN CNV" 
        TCGA-CG-4437         TCGA-CG-4438         TCGA-CG-4440 
"20Q GAIN WILD-TYPE"       "20Q GAIN CNV"       "20Q GAIN CNV" 
        TCGA-CG-4441         TCGA-CG-4443         TCGA-CG-4444 
      "20Q GAIN CNV" "20Q GAIN WILD-TYPE"       "20Q GAIN CNV" 
        TCGA-CG-4449         TCGA-CG-4455         TCGA-CG-4460 
"20Q GAIN WILD-TYPE"       "20Q GAIN CNV" "20Q GAIN WILD-TYPE" 
        TCGA-CG-4462         TCGA-CG-4465         TCGA-CG-4466 
"20Q GAIN WILD-TYPE" "20Q GAIN WILD-TYPE"       "20Q GAIN CNV" 
        TCGA-CG-4469         TCGA-CG-4472         TCGA-CG-4474 
      "20Q GAIN CNV" "20Q GAIN WILD-TYPE" "20Q GAIN WILD-TYPE" 
        TCGA-CG-4477         TCGA-CG-5716         TCGA-CG-5717 
"20Q GAIN WILD-TYPE" "20Q GAIN WILD-TYPE" "20Q GAIN WILD-TYPE" 
        TCGA-CG-5718         TCGA-CG-5719         TCGA-CG-5720 
      "20Q GAIN CNV" "20Q GAIN WILD-TYPE" "20Q GAIN WILD-TYPE" 
        TCGA-CG-5721         TCGA-CG-5722         TCGA-CG-5723 
"20Q GAIN WILD-TYPE" "20Q GAIN WILD-TYPE" "20Q GAIN WILD-TYPE" 
        TCGA-CG-5724         TCGA-CG-5725         TCGA-CG-5726 
      "20Q GAIN CNV" "20Q GAIN WILD-TYPE"       "20Q GAIN CNV" 
        TCGA-CG-5727         TCGA-CG-5728         TCGA-CG-5730 
      "20Q GAIN CNV" "20Q GAIN WILD-TYPE"       "20Q GAIN CNV" 
        TCGA-CG-5732         TCGA-CG-5733         TCGA-CG-5734 
      "20Q GAIN CNV" "20Q GAIN WILD-TYPE" "20Q GAIN WILD-TYPE" 
        TCGA-D7-5577         TCGA-D7-5578         TCGA-D7-5579 
      "20Q GAIN CNV"       "20Q GAIN CNV"       "20Q GAIN CNV" 
        TCGA-D7-6518         TCGA-D7-6519         TCGA-D7-6520 
      "20Q GAIN CNV" "20Q GAIN WILD-TYPE"       "20Q GAIN CNV" 
        TCGA-D7-6521         TCGA-D7-6522         TCGA-D7-6524 
      "20Q GAIN CNV" "20Q GAIN WILD-TYPE" "20Q GAIN WILD-TYPE" 
        TCGA-D7-6525         TCGA-D7-6526         TCGA-D7-6527 
      "20Q GAIN CNV"       "20Q GAIN CNV" "20Q GAIN WILD-TYPE" 
        TCGA-D7-6528         TCGA-D7-6815         TCGA-D7-6817 
      "20Q GAIN CNV"       "20Q GAIN CNV" "20Q GAIN WILD-TYPE" 
        TCGA-D7-6818         TCGA-D7-6820         TCGA-D7-6822 
      "20Q GAIN CNV" "20Q GAIN WILD-TYPE"       "20Q GAIN CNV" 
        TCGA-EQ-5647         TCGA-EQ-8122         TCGA-F1-6177 
"20Q GAIN WILD-TYPE"       "20Q GAIN CNV" "20Q GAIN WILD-TYPE" 
        TCGA-F1-6874         TCGA-F1-6875         TCGA-FP-7735 
      "20Q GAIN CNV"       "20Q GAIN CNV"       "20Q GAIN CNV" 
        TCGA-FP-7829         TCGA-FP-7916         TCGA-FP-7998 
      "20Q GAIN CNV"       "20Q GAIN CNV"       "20Q GAIN CNV" 
        TCGA-FP-8099         TCGA-FP-8209         TCGA-FP-8210 
      "20Q GAIN CNV" "20Q GAIN WILD-TYPE" "20Q GAIN WILD-TYPE" 
        TCGA-FP-8631         TCGA-HJ-7597         TCGA-IN-7806 
      "20Q GAIN CNV" "20Q GAIN WILD-TYPE"       "20Q GAIN CNV" 
        TCGA-IN-7808         TCGA-IP-7968 
      "20Q GAIN CNV"       "20Q GAIN CNV" 
        TCGA-B7-5816         TCGA-B7-5818         TCGA-BR-6452 
"20Q GAIN WILD-TYPE" "20Q GAIN WILD-TYPE" "20Q GAIN WILD-TYPE" 
        TCGA-BR-6455         TCGA-BR-6457         TCGA-BR-6458 
      "20Q GAIN CNV" "20Q GAIN WILD-TYPE"       "20Q GAIN CNV" 
        TCGA-BR-6563         TCGA-BR-6564         TCGA-BR-6565 
"20Q GAIN WILD-TYPE" "20Q GAIN WILD-TYPE"       "20Q GAIN CNV" 
        TCGA-BR-6566         TCGA-BR-6705         TCGA-BR-6706 
"20Q GAIN WILD-TYPE" "20Q GAIN WILD-TYPE"       "20Q GAIN CNV" 
        TCGA-BR-6707         TCGA-BR-6709         TCGA-BR-6710 
      "20Q GAIN CNV" "20Q GAIN WILD-TYPE" "20Q GAIN WILD-TYPE" 
        TCGA-BR-6801         TCGA-BR-6802         TCGA-BR-6803 
      "20Q GAIN CNV" "20Q GAIN WILD-TYPE" "20Q GAIN WILD-TYPE" 
        TCGA-BR-6852         TCGA-BR-7196         TCGA-BR-7197 
"20Q GAIN WILD-TYPE" "20Q GAIN WILD-TYPE"       "20Q GAIN CNV" 
        TCGA-BR-7703         TCGA-BR-7704         TCGA-BR-7707 
"20Q GAIN WILD-TYPE"       "20Q GAIN CNV" "20Q GAIN WILD-TYPE" 
        TCGA-BR-7715         TCGA-BR-7716         TCGA-BR-7717 
      "20Q GAIN CNV" "20Q GAIN WILD-TYPE"       "20Q GAIN CNV" 
        TCGA-BR-7722         TCGA-BR-7723         TCGA-BR-7851 
      "20Q GAIN CNV"       "20Q GAIN CNV" "20Q GAIN WILD-TYPE" 
        TCGA-BR-7901         TCGA-BR-7957         TCGA-BR-7958 
      "20Q GAIN CNV" "20Q GAIN WILD-TYPE"       "20Q GAIN CNV" 
        TCGA-BR-7959         TCGA-BR-8059         TCGA-BR-8060 
      "20Q GAIN CNV"       "20Q GAIN CNV"       "20Q GAIN CNV" 
        TCGA-BR-8077         TCGA-BR-8078         TCGA-BR-8080 
      "20Q GAIN CNV" "20Q GAIN WILD-TYPE" "20Q GAIN WILD-TYPE" 
        TCGA-BR-8081         TCGA-BR-8284         TCGA-BR-8285 
"20Q GAIN WILD-TYPE" "20Q GAIN WILD-TYPE" "20Q GAIN WILD-TYPE" 
        TCGA-BR-8286         TCGA-BR-8289         TCGA-BR-8291 
"20Q GAIN WILD-TYPE"       "20Q GAIN CNV" "20Q GAIN WILD-TYPE" 
        TCGA-BR-8295         TCGA-BR-8296         TCGA-BR-8297 
      "20Q GAIN CNV"       "20Q GAIN CNV" "20Q GAIN WILD-TYPE" 
        TCGA-BR-8592         TCGA-BR-A4IU         TCGA-BR-A4IV 
"20Q GAIN WILD-TYPE" "20Q GAIN WILD-TYPE" "20Q GAIN WILD-TYPE" 
        TCGA-BR-A4IY         TCGA-BR-A4IZ         TCGA-BR-A4J1 
"20Q GAIN WILD-TYPE" "20Q GAIN WILD-TYPE"       "20Q GAIN CNV" 
        TCGA-BR-A4J2         TCGA-BR-A4J4         TCGA-BR-A4J5 
"20Q GAIN WILD-TYPE"       "20Q GAIN CNV" "20Q GAIN WILD-TYPE" 
        TCGA-BR-A4J6         TCGA-BR-A4J8         TCGA-BR-A4J9 
"20Q GAIN WILD-TYPE"       "20Q GAIN CNV" "20Q GAIN WILD-TYPE" 
        TCGA-BR-A4PF         TCGA-BR-A4QI         TCGA-BR-A4QL 
      "20Q GAIN CNV"       "20Q GAIN CNV" "20Q GAIN WILD-TYPE" 
        TCGA-CD-5798         TCGA-CD-5799         TCGA-CD-5800 
"20Q GAIN WILD-TYPE"       "20Q GAIN CNV"       "20Q GAIN CNV" 
        TCGA-CD-5801         TCGA-CD-5802         TCGA-CD-5803 
      "20Q GAIN CNV" "20Q GAIN WILD-TYPE" "20Q GAIN WILD-TYPE" 
        TCGA-CG-4300         TCGA-CG-4301         TCGA-CG-4304 
      "20Q GAIN CNV" "20Q GAIN WILD-TYPE"       "20Q GAIN CNV" 
        TCGA-CG-4305         TCGA-CG-4306         TCGA-CG-4436 
      "20Q GAIN CNV" "20Q GAIN WILD-TYPE"       "20Q GAIN CNV" 
        TCGA-CG-4437         TCGA-CG-4438         TCGA-CG-4440 
"20Q GAIN WILD-TYPE"       "20Q GAIN CNV"       "20Q GAIN CNV" 
        TCGA-CG-4441         TCGA-CG-4443         TCGA-CG-4444 
      "20Q GAIN CNV" "20Q GAIN WILD-TYPE"       "20Q GAIN CNV" 
        TCGA-CG-4449         TCGA-CG-4455         TCGA-CG-4460 
"20Q GAIN WILD-TYPE"       "20Q GAIN CNV" "20Q GAIN WILD-TYPE" 
        TCGA-CG-4462         TCGA-CG-4465         TCGA-CG-4466 
"20Q GAIN WILD-TYPE" "20Q GAIN WILD-TYPE"       "20Q GAIN CNV" 
        TCGA-CG-4469         TCGA-CG-4472         TCGA-CG-4474 
      "20Q GAIN CNV" "20Q GAIN WILD-TYPE" "20Q GAIN WILD-TYPE" 
        TCGA-CG-4477         TCGA-CG-5716         TCGA-CG-5717 
"20Q GAIN WILD-TYPE" "20Q GAIN WILD-TYPE" "20Q GAIN WILD-TYPE" 
        TCGA-CG-5718         TCGA-CG-5719         TCGA-CG-5720 
      "20Q GAIN CNV" "20Q GAIN WILD-TYPE" "20Q GAIN WILD-TYPE" 
        TCGA-CG-5721         TCGA-CG-5722         TCGA-CG-5723 
"20Q GAIN WILD-TYPE" "20Q GAIN WILD-TYPE" "20Q GAIN WILD-TYPE" 
        TCGA-CG-5724         TCGA-CG-5725         TCGA-CG-5726 
      "20Q GAIN CNV" "20Q GAIN WILD-TYPE"       "20Q GAIN CNV" 
        TCGA-CG-5727         TCGA-CG-5728         TCGA-CG-5730 
      "20Q GAIN CNV" "20Q GAIN WILD-TYPE"       "20Q GAIN CNV" 
        TCGA-CG-5732         TCGA-CG-5733         TCGA-CG-5734 
      "20Q GAIN CNV" "20Q GAIN WILD-TYPE" "20Q GAIN WILD-TYPE" 
        TCGA-D7-5577         TCGA-D7-5578         TCGA-D7-5579 
      "20Q GAIN CNV"       "20Q GAIN CNV"       "20Q GAIN CNV" 
        TCGA-D7-6518         TCGA-D7-6519         TCGA-D7-6520 
      "20Q GAIN CNV" "20Q GAIN WILD-TYPE"       "20Q GAIN CNV" 
        TCGA-D7-6521         TCGA-D7-6522         TCGA-D7-6524 
      "20Q GAIN CNV" "20Q GAIN WILD-TYPE" "20Q GAIN WILD-TYPE" 
        TCGA-D7-6525         TCGA-D7-6526         TCGA-D7-6527 
      "20Q GAIN CNV"       "20Q GAIN CNV" "20Q GAIN WILD-TYPE" 
        TCGA-D7-6528         TCGA-D7-6815         TCGA-D7-6817 
      "20Q GAIN CNV"       "20Q GAIN CNV" "20Q GAIN WILD-TYPE" 
        TCGA-D7-6818         TCGA-D7-6820         TCGA-D7-6822 
      "20Q GAIN CNV" "20Q GAIN WILD-TYPE"       "20Q GAIN CNV" 
        TCGA-EQ-5647         TCGA-EQ-8122         TCGA-F1-6177 
"20Q GAIN WILD-TYPE"       "20Q GAIN CNV" "20Q GAIN WILD-TYPE" 
        TCGA-F1-6874         TCGA-F1-6875         TCGA-FP-7735 
      "20Q GAIN CNV"       "20Q GAIN CNV"       "20Q GAIN CNV" 
        TCGA-FP-7829         TCGA-FP-7916         TCGA-FP-7998 
      "20Q GAIN CNV"       "20Q GAIN CNV"       "20Q GAIN CNV" 
        TCGA-FP-8099         TCGA-FP-8209         TCGA-FP-8210 
      "20Q GAIN CNV" "20Q GAIN WILD-TYPE" "20Q GAIN WILD-TYPE" 
        TCGA-FP-8631         TCGA-HJ-7597         TCGA-IN-7806 
      "20Q GAIN CNV" "20Q GAIN WILD-TYPE"       "20Q GAIN CNV" 
        TCGA-IN-7808         TCGA-IP-7968 
      "20Q GAIN CNV"       "20Q GAIN CNV" 
        TCGA-B7-5816         TCGA-B7-5818         TCGA-BR-6452 
"20Q GAIN WILD-TYPE" "20Q GAIN WILD-TYPE" "20Q GAIN WILD-TYPE" 
        TCGA-BR-6455         TCGA-BR-6457         TCGA-BR-6458 
      "20Q GAIN CNV" "20Q GAIN WILD-TYPE"       "20Q GAIN CNV" 
        TCGA-BR-6563         TCGA-BR-6564         TCGA-BR-6565 
"20Q GAIN WILD-TYPE" "20Q GAIN WILD-TYPE"       "20Q GAIN CNV" 
        TCGA-BR-6566         TCGA-BR-6705         TCGA-BR-6706 
"20Q GAIN WILD-TYPE" "20Q GAIN WILD-TYPE"       "20Q GAIN CNV" 
        TCGA-BR-6707         TCGA-BR-6709         TCGA-BR-6710 
      "20Q GAIN CNV" "20Q GAIN WILD-TYPE" "20Q GAIN WILD-TYPE" 
        TCGA-BR-6801         TCGA-BR-6802         TCGA-BR-6803 
      "20Q GAIN CNV" "20Q GAIN WILD-TYPE" "20Q GAIN WILD-TYPE" 
        TCGA-BR-6852         TCGA-BR-7196         TCGA-BR-7197 
"20Q GAIN WILD-TYPE" "20Q GAIN WILD-TYPE"       "20Q GAIN CNV" 
        TCGA-BR-7703         TCGA-BR-7704         TCGA-BR-7707 
"20Q GAIN WILD-TYPE"       "20Q GAIN CNV" "20Q GAIN WILD-TYPE" 
        TCGA-BR-7715         TCGA-BR-7716         TCGA-BR-7717 
      "20Q GAIN CNV" "20Q GAIN WILD-TYPE"       "20Q GAIN CNV" 
        TCGA-BR-7722         TCGA-BR-7723         TCGA-BR-7851 
      "20Q GAIN CNV"       "20Q GAIN CNV" "20Q GAIN WILD-TYPE" 
        TCGA-BR-7901         TCGA-BR-7957         TCGA-BR-7958 
      "20Q GAIN CNV" "20Q GAIN WILD-TYPE"       "20Q GAIN CNV" 
        TCGA-BR-7959         TCGA-BR-8059         TCGA-BR-8060 
      "20Q GAIN CNV"       "20Q GAIN CNV"       "20Q GAIN CNV" 
        TCGA-BR-8077         TCGA-BR-8078         TCGA-BR-8080 
      "20Q GAIN CNV" "20Q GAIN WILD-TYPE" "20Q GAIN WILD-TYPE" 
        TCGA-BR-8081         TCGA-BR-8284         TCGA-BR-8285 
"20Q GAIN WILD-TYPE" "20Q GAIN WILD-TYPE" "20Q GAIN WILD-TYPE" 
        TCGA-BR-8286         TCGA-BR-8289         TCGA-BR-8291 
"20Q GAIN WILD-TYPE"       "20Q GAIN CNV" "20Q GAIN WILD-TYPE" 
        TCGA-BR-8295         TCGA-BR-8296         TCGA-BR-8297 
      "20Q GAIN CNV"       "20Q GAIN CNV" "20Q GAIN WILD-TYPE" 
        TCGA-BR-8592         TCGA-BR-A4IU         TCGA-BR-A4IV 
"20Q GAIN WILD-TYPE" "20Q GAIN WILD-TYPE" "20Q GAIN WILD-TYPE" 
        TCGA-BR-A4IY         TCGA-BR-A4IZ         TCGA-BR-A4J1 
"20Q GAIN WILD-TYPE" "20Q GAIN WILD-TYPE"       "20Q GAIN CNV" 
        TCGA-BR-A4J2         TCGA-BR-A4J4         TCGA-BR-A4J5 
"20Q GAIN WILD-TYPE"       "20Q GAIN CNV" "20Q GAIN WILD-TYPE" 
        TCGA-BR-A4J6         TCGA-BR-A4J8         TCGA-BR-A4J9 
"20Q GAIN WILD-TYPE"       "20Q GAIN CNV" "20Q GAIN WILD-TYPE" 
        TCGA-BR-A4PF         TCGA-BR-A4QI         TCGA-BR-A4QL 
      "20Q GAIN CNV"       "20Q GAIN CNV" "20Q GAIN WILD-TYPE" 
        TCGA-CD-5798         TCGA-CD-5799         TCGA-CD-5800 
"20Q GAIN WILD-TYPE"       "20Q GAIN CNV"       "20Q GAIN CNV" 
        TCGA-CD-5801         TCGA-CD-5802         TCGA-CD-5803 
      "20Q GAIN CNV" "20Q GAIN WILD-TYPE" "20Q GAIN WILD-TYPE" 
        TCGA-CG-4300         TCGA-CG-4301         TCGA-CG-4304 
      "20Q GAIN CNV" "20Q GAIN WILD-TYPE"       "20Q GAIN CNV" 
        TCGA-CG-4305         TCGA-CG-4306         TCGA-CG-4436 
      "20Q GAIN CNV" "20Q GAIN WILD-TYPE"       "20Q GAIN CNV" 
        TCGA-CG-4437         TCGA-CG-4438         TCGA-CG-4440 
"20Q GAIN WILD-TYPE"       "20Q GAIN CNV"       "20Q GAIN CNV" 
        TCGA-CG-4441         TCGA-CG-4443         TCGA-CG-4444 
      "20Q GAIN CNV" "20Q GAIN WILD-TYPE"       "20Q GAIN CNV" 
        TCGA-CG-4449         TCGA-CG-4455         TCGA-CG-4460 
"20Q GAIN WILD-TYPE"       "20Q GAIN CNV" "20Q GAIN WILD-TYPE" 
        TCGA-CG-4462         TCGA-CG-4465         TCGA-CG-4466 
"20Q GAIN WILD-TYPE" "20Q GAIN WILD-TYPE"       "20Q GAIN CNV" 
        TCGA-CG-4469         TCGA-CG-4472         TCGA-CG-4474 
      "20Q GAIN CNV" "20Q GAIN WILD-TYPE" "20Q GAIN WILD-TYPE" 
        TCGA-CG-4477         TCGA-CG-5716         TCGA-CG-5717 
"20Q GAIN WILD-TYPE" "20Q GAIN WILD-TYPE" "20Q GAIN WILD-TYPE" 
        TCGA-CG-5718         TCGA-CG-5719         TCGA-CG-5720 
      "20Q GAIN CNV" "20Q GAIN WILD-TYPE" "20Q GAIN WILD-TYPE" 
        TCGA-CG-5721         TCGA-CG-5722         TCGA-CG-5723 
"20Q GAIN WILD-TYPE" "20Q GAIN WILD-TYPE" "20Q GAIN WILD-TYPE" 
        TCGA-CG-5724         TCGA-CG-5725         TCGA-CG-5726 
      "20Q GAIN CNV" "20Q GAIN WILD-TYPE"       "20Q GAIN CNV" 
        TCGA-CG-5727         TCGA-CG-5728         TCGA-CG-5730 
      "20Q GAIN CNV" "20Q GAIN WILD-TYPE"       "20Q GAIN CNV" 
        TCGA-CG-5732         TCGA-CG-5733         TCGA-CG-5734 
      "20Q GAIN CNV" "20Q GAIN WILD-TYPE" "20Q GAIN WILD-TYPE" 
        TCGA-D7-5577         TCGA-D7-5578         TCGA-D7-5579 
      "20Q GAIN CNV"       "20Q GAIN CNV"       "20Q GAIN CNV" 
        TCGA-D7-6518         TCGA-D7-6519         TCGA-D7-6520 
      "20Q GAIN CNV" "20Q GAIN WILD-TYPE"       "20Q GAIN CNV" 
        TCGA-D7-6521         TCGA-D7-6522         TCGA-D7-6524 
      "20Q GAIN CNV" "20Q GAIN WILD-TYPE" "20Q GAIN WILD-TYPE" 
        TCGA-D7-6525         TCGA-D7-6526         TCGA-D7-6527 
      "20Q GAIN CNV"       "20Q GAIN CNV" "20Q GAIN WILD-TYPE" 
        TCGA-D7-6528         TCGA-D7-6815         TCGA-D7-6817 
      "20Q GAIN CNV"       "20Q GAIN CNV" "20Q GAIN WILD-TYPE" 
        TCGA-D7-6818         TCGA-D7-6820         TCGA-D7-6822 
      "20Q GAIN CNV" "20Q GAIN WILD-TYPE"       "20Q GAIN CNV" 
        TCGA-EQ-5647         TCGA-EQ-8122         TCGA-F1-6177 
"20Q GAIN WILD-TYPE"       "20Q GAIN CNV" "20Q GAIN WILD-TYPE" 
        TCGA-F1-6874         TCGA-F1-6875         TCGA-FP-7735 
      "20Q GAIN CNV"       "20Q GAIN CNV"       "20Q GAIN CNV" 
        TCGA-FP-7829         TCGA-FP-7916         TCGA-FP-7998 
      "20Q GAIN CNV"       "20Q GAIN CNV"       "20Q GAIN CNV" 
        TCGA-FP-8099         TCGA-FP-8209         TCGA-FP-8210 
      "20Q GAIN CNV" "20Q GAIN WILD-TYPE" "20Q GAIN WILD-TYPE" 
        TCGA-FP-8631         TCGA-HJ-7597         TCGA-IN-7806 
      "20Q GAIN CNV" "20Q GAIN WILD-TYPE"       "20Q GAIN CNV" 
        TCGA-IN-7808         TCGA-IP-7968 
      "20Q GAIN CNV"       "20Q GAIN CNV" 
[1] "hr=" "2.5"
D36V2, continuous
D36V3, binary
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  20Q GAIN CNV         26   64
  20Q GAIN WILD-TYPE   46   44
        clus
vv       20Q GAIN CNV 20Q GAIN WILD-TYPE
  FEMALE           26                 46
  MALE             64                 44
                    vv
clus                 STOMACH  ADENOCARCINOMA  DIFFUSE TYPE
  20Q GAIN CNV                                           1
  20Q GAIN WILD-TYPE                                     9
                    vv
clus                 STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  20Q GAIN CNV                                                            9
  20Q GAIN WILD-TYPE                                                      7
                    vv
clus                 STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  20Q GAIN CNV                                                                       6
  20Q GAIN WILD-TYPE                                                                 2
                    vv
clus                 STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE
  20Q GAIN CNV                                                              1
  20Q GAIN WILD-TYPE                                                        2
                    vv
clus                 STOMACH ADENOCARCINOMA  SIGNET RING TYPE
  20Q GAIN CNV                                              0
  20Q GAIN WILD-TYPE                                        1
                    vv
clus                 STOMACH ADENOCARCINOMA - DIFFUSE TYPE
  20Q GAIN CNV                                           9
  20Q GAIN WILD-TYPE                                     7
                    vv
clus                 STOMACH ADENOCARCINOMA - NOT OTHERWISE SPECIFIED (NOS)
  20Q GAIN CNV                                                           35
  20Q GAIN WILD-TYPE                                                     38
                    vv
clus                 STOMACH INTESTINAL ADENOCARCINOMA - MUCINOUS TYPE
  20Q GAIN CNV                                                       3
  20Q GAIN WILD-TYPE                                                 4
                    vv
clus                 STOMACH INTESTINAL ADENOCARCINOMA - PAPILLARY TYPE
  20Q GAIN CNV                                                        1
  20Q GAIN WILD-TYPE                                                  2
                    vv
clus                 STOMACH INTESTINAL ADENOCARCINOMA - TUBULAR TYPE
  20Q GAIN CNV                                                      8
  20Q GAIN WILD-TYPE                                                2
                    vv
clus                 STOMACH INTESTINAL ADENOCARCINOMA - TYPE NOT OTHERWISE SPECIFIED (NOS)
  20Q GAIN CNV                                                                           15
  20Q GAIN WILD-TYPE                                                                     13
D36V4, multiclass
                    vv
clus                 T1 T2 T3 T4
  20Q GAIN CNV        2 28 34  5
  20Q GAIN WILD-TYPE  4 24 22 13
D36V5, multiclass
    clus
vv   20Q GAIN CNV 20Q GAIN WILD-TYPE
  T1            2                  4
  T2           28                 24
  T3           34                 22
  T4            5                 13
                    vv
clus                 N0 N1 N2 N3
  20Q GAIN CNV       20 24 13 10
  20Q GAIN WILD-TYPE 24 25 10  5
D36V6, multiclass
    clus
vv   20Q GAIN CNV 20Q GAIN WILD-TYPE
  N0           20                 24
  N1           24                 25
  N2           13                 10
  N3           10                  5
                    vv
clus                 M0 M1 MX
  20Q GAIN CNV       63  4  6
  20Q GAIN WILD-TYPE 55 12  2
D36V7, multiclass
    clus
vv   20Q GAIN CNV 20Q GAIN WILD-TYPE
  M0           63                 55
  M1            4                 12
  MX            6                  2
                    vv
clus                  I II III IV
  20Q GAIN CNV       11 18  27  9
  20Q GAIN WILD-TYPE 13 19  12 17
D36V8, multiclass
     clus
vv    20Q GAIN CNV 20Q GAIN WILD-TYPE
  I             11                 13
  II            18                 19
  III           27                 12
  IV             9                 17
D36V9, binary
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  20Q GAIN CNV          2   88
  20Q GAIN WILD-TYPE    3   87
     clus
vv    20Q GAIN CNV 20Q GAIN WILD-TYPE
  NO             2                  3
  YES           88                 87
                    vv
clus                 R0 R1 R2 RX
  20Q GAIN CNV       64  4  3 12
  20Q GAIN WILD-TYPE 61  3  9 13
D36V10, multiclass
    clus
vv   20Q GAIN CNV 20Q GAIN WILD-TYPE
  R0           64                 61
  R1            4                  3
  R2            3                  9
  RX           12                 13
D36V11, continuous

Clustering(37) Variable = 22q gain
D37V1, survival
                    sevent
clus2                  0   1
  22Q GAIN CNV         3   0
  22Q GAIN WILD-TYPE 121  19
      22Q GAIN CNV 22Q GAIN WILD-TYPE 
                 3                140 
      22Q GAIN CNV 22Q GAIN WILD-TYPE 
                 0                 19 
$`22Q GAIN CNV`
TCGA-B7-5818 TCGA-BR-7704 TCGA-BR-7723 
        0.10         1.25         4.54 

$`22Q GAIN WILD-TYPE`
TCGA-B7-5816 TCGA-BR-6452 TCGA-BR-6455 TCGA-BR-6457 TCGA-BR-6458 TCGA-BR-6563 
        5.62         0.95         1.41         1.35         1.35         0.85 
TCGA-BR-6564 TCGA-BR-6565 TCGA-BR-6566 TCGA-BR-6705 TCGA-BR-6706 TCGA-BR-6707 
        0.82         0.62         0.62         1.71         2.17         0.99 
TCGA-BR-6709 TCGA-BR-6710 TCGA-BR-6801 TCGA-BR-6802 TCGA-BR-6803 TCGA-BR-6852 
        1.22         0.66         1.12         0.76         0.66         0.26 
TCGA-BR-7196 TCGA-BR-7197 TCGA-BR-7703 TCGA-BR-7707 TCGA-BR-7715 TCGA-BR-7716 
        1.22         1.48         0.46         0.13         1.05         0.82 
TCGA-BR-7717 TCGA-BR-7722 TCGA-BR-7851 TCGA-BR-7901 TCGA-BR-7957 TCGA-BR-7958 
        0.69         0.16         0.99         0.95         0.69         0.16 
TCGA-BR-7959 TCGA-BR-8059 TCGA-BR-8060 TCGA-BR-8077 TCGA-BR-8078 TCGA-BR-8080 
        1.08         0.82         1.32         0.69         0.95         0.49 
TCGA-BR-8081 TCGA-BR-8284 TCGA-BR-8285 TCGA-BR-8286 TCGA-BR-8289 TCGA-BR-8291 
        0.46         0.72         0.26         0.43         0.26         1.18 
TCGA-BR-8295 TCGA-BR-8296 TCGA-BR-8297 TCGA-BR-8592 TCGA-BR-A4IU TCGA-BR-A4IV 
        1.55         1.48         0.76         0.20         0.59         0.92 
TCGA-BR-A4IY TCGA-BR-A4IZ TCGA-BR-A4J1 TCGA-BR-A4J2 TCGA-BR-A4J4 TCGA-BR-A4J5 
        0.39         0.79         0.72         0.79         0.53         0.43 
TCGA-BR-A4J6 TCGA-BR-A4J8 TCGA-BR-A4J9 TCGA-BR-A4PF TCGA-BR-A4QI TCGA-BR-A4QL 
        0.13         0.23         0.10         0.72         0.49         2.24 
TCGA-CD-5798 TCGA-CD-5799 TCGA-CD-5800 TCGA-CD-5801 TCGA-CD-5802 TCGA-CD-5803 
        0.82         0.69         0.36         0.49         0.30         0.07 
TCGA-CG-4300 TCGA-CG-4301 TCGA-CG-4304 TCGA-CG-4305 TCGA-CG-4306 TCGA-CG-4436 
       20.02         3.02        27.02        15.95         1.02        52.96 
TCGA-CG-4437 TCGA-CG-4438 TCGA-CG-4440 TCGA-CG-4441 TCGA-CG-4443 TCGA-CG-4444 
        8.05        54.05         4.01        14.01        29.98        47.05 
TCGA-CG-4449 TCGA-CG-4455 TCGA-CG-4460 TCGA-CG-4462 TCGA-CG-4465 TCGA-CG-4466 
       19.07        12.03        21.99         1.02         8.98        18.94 
TCGA-CG-4469 TCGA-CG-4472 TCGA-CG-4474 TCGA-CG-4477 TCGA-CG-5716 TCGA-CG-5717 
        7.07        12.00         1.02         1.02         1.02         6.94 
TCGA-CG-5718 TCGA-CG-5719 TCGA-CG-5720 TCGA-CG-5721 TCGA-CG-5722 TCGA-CG-5723 
        1.02         1.02         0.99         5.98         0.95        70.06 
TCGA-CG-5724 TCGA-CG-5725 TCGA-CG-5726 TCGA-CG-5727 TCGA-CG-5728 TCGA-CG-5730 
       12.03        15.02        28.96        31.04        65.10         4.01 
TCGA-CG-5732 TCGA-CG-5733 TCGA-CG-5734 TCGA-D7-5577 TCGA-D7-5578 TCGA-D7-5579 
       55.04        21.07         7.99         8.65         3.58         4.54 
TCGA-D7-6518 TCGA-D7-6519 TCGA-D7-6520 TCGA-D7-6521 TCGA-D7-6522 TCGA-D7-6524 
        9.80        15.65         9.63         8.19         6.90         0.69 
TCGA-D7-6525 TCGA-D7-6526 TCGA-D7-6527 TCGA-D7-6528 TCGA-D7-6815 TCGA-D7-6817 
        5.95         6.61         4.14         1.68         3.65         4.70 
TCGA-D7-6818 TCGA-D7-6820 TCGA-D7-6822 TCGA-EQ-5647 TCGA-EQ-8122 TCGA-F1-6177 
        4.04         2.93         4.27         0.62         7.79         6.54 
TCGA-F1-6874 TCGA-F1-6875 TCGA-FP-7735 TCGA-FP-7829 TCGA-FP-7916 TCGA-FP-7998 
        2.01        72.23         0.39         0.20         3.02         3.58 
TCGA-FP-8099 TCGA-FP-8209 TCGA-FP-8210 TCGA-FP-8631 TCGA-HJ-7597 TCGA-IN-7806 
        1.02        59.05         5.03         0.56        26.43         6.87 
TCGA-IN-7808 TCGA-IP-7968 
        3.55         2.53 

      22Q GAIN CNV 22Q GAIN WILD-TYPE 
              0.10               0.07 
      22Q GAIN CNV 22Q GAIN WILD-TYPE 
              4.54              72.23 
      22Q GAIN CNV 22Q GAIN WILD-TYPE 
              1.25               1.27 
[1] "0.1 - 4.5 (1.2)"  "0.1 - 72.2 (1.3)"
        TCGA-B7-5816         TCGA-B7-5818         TCGA-BR-6452 
"22Q GAIN WILD-TYPE"       "22Q GAIN CNV" "22Q GAIN WILD-TYPE" 
        TCGA-BR-6455         TCGA-BR-6457         TCGA-BR-6458 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-BR-6563         TCGA-BR-6564         TCGA-BR-6565 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-BR-6566         TCGA-BR-6705         TCGA-BR-6706 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-BR-6707         TCGA-BR-6709         TCGA-BR-6710 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-BR-6801         TCGA-BR-6802         TCGA-BR-6803 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-BR-6852         TCGA-BR-7196         TCGA-BR-7197 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-BR-7703         TCGA-BR-7704         TCGA-BR-7707 
"22Q GAIN WILD-TYPE"       "22Q GAIN CNV" "22Q GAIN WILD-TYPE" 
        TCGA-BR-7715         TCGA-BR-7716         TCGA-BR-7717 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-BR-7722         TCGA-BR-7723         TCGA-BR-7851 
"22Q GAIN WILD-TYPE"       "22Q GAIN CNV" "22Q GAIN WILD-TYPE" 
        TCGA-BR-7901         TCGA-BR-7957         TCGA-BR-7958 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-BR-7959         TCGA-BR-8059         TCGA-BR-8060 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-BR-8077         TCGA-BR-8078         TCGA-BR-8080 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-BR-8081         TCGA-BR-8284         TCGA-BR-8285 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-BR-8286         TCGA-BR-8289         TCGA-BR-8291 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-BR-8295         TCGA-BR-8296         TCGA-BR-8297 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-BR-8592         TCGA-BR-A4IU         TCGA-BR-A4IV 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-BR-A4IY         TCGA-BR-A4IZ         TCGA-BR-A4J1 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-BR-A4J2         TCGA-BR-A4J4         TCGA-BR-A4J5 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-BR-A4J6         TCGA-BR-A4J8         TCGA-BR-A4J9 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-BR-A4PF         TCGA-BR-A4QI         TCGA-BR-A4QL 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-CD-5798         TCGA-CD-5799         TCGA-CD-5800 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-CD-5801         TCGA-CD-5802         TCGA-CD-5803 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-CG-4300         TCGA-CG-4301         TCGA-CG-4304 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-CG-4305         TCGA-CG-4306         TCGA-CG-4436 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-CG-4437         TCGA-CG-4438         TCGA-CG-4440 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-CG-4441         TCGA-CG-4443         TCGA-CG-4444 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-CG-4449         TCGA-CG-4455         TCGA-CG-4460 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-CG-4462         TCGA-CG-4465         TCGA-CG-4466 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-CG-4469         TCGA-CG-4472         TCGA-CG-4474 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-CG-4477         TCGA-CG-5716         TCGA-CG-5717 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-CG-5718         TCGA-CG-5719         TCGA-CG-5720 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-CG-5721         TCGA-CG-5722         TCGA-CG-5723 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-CG-5724         TCGA-CG-5725         TCGA-CG-5726 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-CG-5727         TCGA-CG-5728         TCGA-CG-5730 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-CG-5732         TCGA-CG-5733         TCGA-CG-5734 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-D7-5577         TCGA-D7-5578         TCGA-D7-5579 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-D7-6518         TCGA-D7-6519         TCGA-D7-6520 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-D7-6521         TCGA-D7-6522         TCGA-D7-6524 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-D7-6525         TCGA-D7-6526         TCGA-D7-6527 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-D7-6528         TCGA-D7-6815         TCGA-D7-6817 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-D7-6818         TCGA-D7-6820         TCGA-D7-6822 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-EQ-5647         TCGA-EQ-8122         TCGA-F1-6177 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-F1-6874         TCGA-F1-6875         TCGA-FP-7735 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-FP-7829         TCGA-FP-7916         TCGA-FP-7998 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-FP-8099         TCGA-FP-8209         TCGA-FP-8210 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-FP-8631         TCGA-HJ-7597         TCGA-IN-7806 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-IN-7808         TCGA-IP-7968 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-B7-5816         TCGA-B7-5818         TCGA-BR-6452 
"22Q GAIN WILD-TYPE"       "22Q GAIN CNV" "22Q GAIN WILD-TYPE" 
        TCGA-BR-6455         TCGA-BR-6457         TCGA-BR-6458 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-BR-6563         TCGA-BR-6564         TCGA-BR-6565 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-BR-6566         TCGA-BR-6705         TCGA-BR-6706 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-BR-6707         TCGA-BR-6709         TCGA-BR-6710 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-BR-6801         TCGA-BR-6802         TCGA-BR-6803 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-BR-6852         TCGA-BR-7196         TCGA-BR-7197 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-BR-7703         TCGA-BR-7704         TCGA-BR-7707 
"22Q GAIN WILD-TYPE"       "22Q GAIN CNV" "22Q GAIN WILD-TYPE" 
        TCGA-BR-7715         TCGA-BR-7716         TCGA-BR-7717 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-BR-7722         TCGA-BR-7723         TCGA-BR-7851 
"22Q GAIN WILD-TYPE"       "22Q GAIN CNV" "22Q GAIN WILD-TYPE" 
        TCGA-BR-7901         TCGA-BR-7957         TCGA-BR-7958 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-BR-7959         TCGA-BR-8059         TCGA-BR-8060 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-BR-8077         TCGA-BR-8078         TCGA-BR-8080 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-BR-8081         TCGA-BR-8284         TCGA-BR-8285 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-BR-8286         TCGA-BR-8289         TCGA-BR-8291 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-BR-8295         TCGA-BR-8296         TCGA-BR-8297 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-BR-8592         TCGA-BR-A4IU         TCGA-BR-A4IV 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-BR-A4IY         TCGA-BR-A4IZ         TCGA-BR-A4J1 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-BR-A4J2         TCGA-BR-A4J4         TCGA-BR-A4J5 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-BR-A4J6         TCGA-BR-A4J8         TCGA-BR-A4J9 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-BR-A4PF         TCGA-BR-A4QI         TCGA-BR-A4QL 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-CD-5798         TCGA-CD-5799         TCGA-CD-5800 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-CD-5801         TCGA-CD-5802         TCGA-CD-5803 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-CG-4300         TCGA-CG-4301         TCGA-CG-4304 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-CG-4305         TCGA-CG-4306         TCGA-CG-4436 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-CG-4437         TCGA-CG-4438         TCGA-CG-4440 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-CG-4441         TCGA-CG-4443         TCGA-CG-4444 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-CG-4449         TCGA-CG-4455         TCGA-CG-4460 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-CG-4462         TCGA-CG-4465         TCGA-CG-4466 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-CG-4469         TCGA-CG-4472         TCGA-CG-4474 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-CG-4477         TCGA-CG-5716         TCGA-CG-5717 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-CG-5718         TCGA-CG-5719         TCGA-CG-5720 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-CG-5721         TCGA-CG-5722         TCGA-CG-5723 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-CG-5724         TCGA-CG-5725         TCGA-CG-5726 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-CG-5727         TCGA-CG-5728         TCGA-CG-5730 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-CG-5732         TCGA-CG-5733         TCGA-CG-5734 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-D7-5577         TCGA-D7-5578         TCGA-D7-5579 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-D7-6518         TCGA-D7-6519         TCGA-D7-6520 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-D7-6521         TCGA-D7-6522         TCGA-D7-6524 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-D7-6525         TCGA-D7-6526         TCGA-D7-6527 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-D7-6528         TCGA-D7-6815         TCGA-D7-6817 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-D7-6818         TCGA-D7-6820         TCGA-D7-6822 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-EQ-5647         TCGA-EQ-8122         TCGA-F1-6177 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-F1-6874         TCGA-F1-6875         TCGA-FP-7735 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-FP-7829         TCGA-FP-7916         TCGA-FP-7998 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-FP-8099         TCGA-FP-8209         TCGA-FP-8210 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-FP-8631         TCGA-HJ-7597         TCGA-IN-7806 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-IN-7808         TCGA-IP-7968 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-B7-5816         TCGA-B7-5818         TCGA-BR-6452 
"22Q GAIN WILD-TYPE"       "22Q GAIN CNV" "22Q GAIN WILD-TYPE" 
        TCGA-BR-6455         TCGA-BR-6457         TCGA-BR-6458 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-BR-6563         TCGA-BR-6564         TCGA-BR-6565 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-BR-6566         TCGA-BR-6705         TCGA-BR-6706 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-BR-6707         TCGA-BR-6709         TCGA-BR-6710 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-BR-6801         TCGA-BR-6802         TCGA-BR-6803 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-BR-6852         TCGA-BR-7196         TCGA-BR-7197 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-BR-7703         TCGA-BR-7704         TCGA-BR-7707 
"22Q GAIN WILD-TYPE"       "22Q GAIN CNV" "22Q GAIN WILD-TYPE" 
        TCGA-BR-7715         TCGA-BR-7716         TCGA-BR-7717 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-BR-7722         TCGA-BR-7723         TCGA-BR-7851 
"22Q GAIN WILD-TYPE"       "22Q GAIN CNV" "22Q GAIN WILD-TYPE" 
        TCGA-BR-7901         TCGA-BR-7957         TCGA-BR-7958 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-BR-7959         TCGA-BR-8059         TCGA-BR-8060 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-BR-8077         TCGA-BR-8078         TCGA-BR-8080 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-BR-8081         TCGA-BR-8284         TCGA-BR-8285 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-BR-8286         TCGA-BR-8289         TCGA-BR-8291 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-BR-8295         TCGA-BR-8296         TCGA-BR-8297 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-BR-8592         TCGA-BR-A4IU         TCGA-BR-A4IV 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-BR-A4IY         TCGA-BR-A4IZ         TCGA-BR-A4J1 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-BR-A4J2         TCGA-BR-A4J4         TCGA-BR-A4J5 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-BR-A4J6         TCGA-BR-A4J8         TCGA-BR-A4J9 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-BR-A4PF         TCGA-BR-A4QI         TCGA-BR-A4QL 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-CD-5798         TCGA-CD-5799         TCGA-CD-5800 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-CD-5801         TCGA-CD-5802         TCGA-CD-5803 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-CG-4300         TCGA-CG-4301         TCGA-CG-4304 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-CG-4305         TCGA-CG-4306         TCGA-CG-4436 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-CG-4437         TCGA-CG-4438         TCGA-CG-4440 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-CG-4441         TCGA-CG-4443         TCGA-CG-4444 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-CG-4449         TCGA-CG-4455         TCGA-CG-4460 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-CG-4462         TCGA-CG-4465         TCGA-CG-4466 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-CG-4469         TCGA-CG-4472         TCGA-CG-4474 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-CG-4477         TCGA-CG-5716         TCGA-CG-5717 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-CG-5718         TCGA-CG-5719         TCGA-CG-5720 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-CG-5721         TCGA-CG-5722         TCGA-CG-5723 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-CG-5724         TCGA-CG-5725         TCGA-CG-5726 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-CG-5727         TCGA-CG-5728         TCGA-CG-5730 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-CG-5732         TCGA-CG-5733         TCGA-CG-5734 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-D7-5577         TCGA-D7-5578         TCGA-D7-5579 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-D7-6518         TCGA-D7-6519         TCGA-D7-6520 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-D7-6521         TCGA-D7-6522         TCGA-D7-6524 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-D7-6525         TCGA-D7-6526         TCGA-D7-6527 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-D7-6528         TCGA-D7-6815         TCGA-D7-6817 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-D7-6818         TCGA-D7-6820         TCGA-D7-6822 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-EQ-5647         TCGA-EQ-8122         TCGA-F1-6177 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-F1-6874         TCGA-F1-6875         TCGA-FP-7735 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-FP-7829         TCGA-FP-7916         TCGA-FP-7998 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-FP-8099         TCGA-FP-8209         TCGA-FP-8210 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-FP-8631         TCGA-HJ-7597         TCGA-IN-7806 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-IN-7808         TCGA-IP-7968 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
[1] "hr="     "3400000"
D37V2, continuous
D37V3, binary
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  22Q GAIN CNV          1    2
  22Q GAIN WILD-TYPE   71  106
        clus
vv       22Q GAIN CNV 22Q GAIN WILD-TYPE
  FEMALE            1                 71
  MALE              2                106
                    vv
clus                 STOMACH  ADENOCARCINOMA  DIFFUSE TYPE
  22Q GAIN CNV                                           0
  22Q GAIN WILD-TYPE                                    10
                    vv
clus                 STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  22Q GAIN CNV                                                            0
  22Q GAIN WILD-TYPE                                                     16
                    vv
clus                 STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  22Q GAIN CNV                                                                       0
  22Q GAIN WILD-TYPE                                                                 8
                    vv
clus                 STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE
  22Q GAIN CNV                                                              0
  22Q GAIN WILD-TYPE                                                        3
                    vv
clus                 STOMACH ADENOCARCINOMA  SIGNET RING TYPE
  22Q GAIN CNV                                              0
  22Q GAIN WILD-TYPE                                        1
                    vv
clus                 STOMACH ADENOCARCINOMA - DIFFUSE TYPE
  22Q GAIN CNV                                           1
  22Q GAIN WILD-TYPE                                    15
                    vv
clus                 STOMACH ADENOCARCINOMA - NOT OTHERWISE SPECIFIED (NOS)
  22Q GAIN CNV                                                            1
  22Q GAIN WILD-TYPE                                                     72
                    vv
clus                 STOMACH INTESTINAL ADENOCARCINOMA - MUCINOUS TYPE
  22Q GAIN CNV                                                       0
  22Q GAIN WILD-TYPE                                                 7
                    vv
clus                 STOMACH INTESTINAL ADENOCARCINOMA - PAPILLARY TYPE
  22Q GAIN CNV                                                        0
  22Q GAIN WILD-TYPE                                                  3
                    vv
clus                 STOMACH INTESTINAL ADENOCARCINOMA - TUBULAR TYPE
  22Q GAIN CNV                                                      0
  22Q GAIN WILD-TYPE                                               10
                    vv
clus                 STOMACH INTESTINAL ADENOCARCINOMA - TYPE NOT OTHERWISE SPECIFIED (NOS)
  22Q GAIN CNV                                                                            1
  22Q GAIN WILD-TYPE                                                                     27
D37V4, multiclass
                    vv
clus                 T1 T2 T3 T4
  22Q GAIN CNV        0  1  2  0
  22Q GAIN WILD-TYPE  6 51 54 18
D37V5, multiclass
    clus
vv   22Q GAIN CNV 22Q GAIN WILD-TYPE
  T1            0                  6
  T2            1                 51
  T3            2                 54
  T4            0                 18
                    vv
clus                 N0 N1 N2 N3
  22Q GAIN CNV        2  0  1  0
  22Q GAIN WILD-TYPE 42 49 22 15
D37V6, multiclass
    clus
vv   22Q GAIN CNV 22Q GAIN WILD-TYPE
  N0            2                 42
  N1            0                 49
  N2            1                 22
  N3            0                 15
                    vv
clus                  M0  M1  MX
  22Q GAIN CNV         3   0   0
  22Q GAIN WILD-TYPE 115  16   8
D37V7, multiclass
    clus
vv   22Q GAIN CNV 22Q GAIN WILD-TYPE
  M0            3                115
  M1            0                 16
  MX            0                  8
                    vv
clus                  I II III IV
  22Q GAIN CNV        1  2   0  0
  22Q GAIN WILD-TYPE 23 35  39 26
D37V8, multiclass
     clus
vv    22Q GAIN CNV 22Q GAIN WILD-TYPE
  I              1                 23
  II             2                 35
  III            0                 39
  IV             0                 26
D37V9, binary
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  22Q GAIN CNV          0    3
  22Q GAIN WILD-TYPE    5  172
     clus
vv    22Q GAIN CNV 22Q GAIN WILD-TYPE
  NO             0                  5
  YES            3                172
                    vv
clus                  R0  R1  R2  RX
  22Q GAIN CNV         3   0   0   0
  22Q GAIN WILD-TYPE 122   7  12  25
D37V10, multiclass
    clus
vv   22Q GAIN CNV 22Q GAIN WILD-TYPE
  R0            3                122
  R1            0                  7
  R2            0                 12
  RX            0                 25
D37V11, continuous
[1] "Remove cluster labels:" "22Q GAIN CNV"          
clus
      22Q GAIN CNV 22Q GAIN WILD-TYPE 
                 2                134 
        TCGA-B7-5816         TCGA-BR-4183         TCGA-BR-4184 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-BR-4188         TCGA-BR-4191         TCGA-BR-4253 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-BR-4255         TCGA-BR-4256         TCGA-BR-4267 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-BR-4279         TCGA-BR-4280         TCGA-BR-4361 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-BR-4362         TCGA-BR-4367         TCGA-BR-4368 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-BR-6452         TCGA-BR-6453         TCGA-BR-6454 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-BR-6455         TCGA-BR-6456         TCGA-BR-6457 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-BR-6458         TCGA-BR-6563         TCGA-BR-6564 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-BR-6565         TCGA-BR-6566         TCGA-BR-6705 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-BR-6706         TCGA-BR-6707         TCGA-BR-6709 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-BR-6710         TCGA-BR-6801         TCGA-BR-6802 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-BR-6803         TCGA-BR-6852         TCGA-BR-7196 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-BR-7197         TCGA-BR-7703         TCGA-BR-7707 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-BR-7715         TCGA-BR-7716         TCGA-BR-7717 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-BR-7722         TCGA-BR-7851         TCGA-BR-7901 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-BR-7957         TCGA-BR-7958         TCGA-BR-7959 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-BR-8059         TCGA-BR-8060         TCGA-BR-8077 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-BR-8078         TCGA-BR-8080         TCGA-BR-8081 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-BR-8284         TCGA-BR-8285         TCGA-BR-8286 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-BR-8289         TCGA-BR-8291         TCGA-BR-8295 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-BR-8296         TCGA-BR-8297         TCGA-BR-8592 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-BR-A4IU         TCGA-BR-A4IV         TCGA-BR-A4IY 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-BR-A4IZ         TCGA-BR-A4J1         TCGA-BR-A4J2 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-BR-A4J4         TCGA-BR-A4J5         TCGA-BR-A4J6 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-BR-A4J8         TCGA-BR-A4J9         TCGA-BR-A4PF 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-BR-A4QI         TCGA-BR-A4QL         TCGA-CD-5804 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-CG-5717         TCGA-CG-5718         TCGA-CG-5719 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-CG-5720         TCGA-CG-5721         TCGA-CG-5722 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-CG-5723         TCGA-CG-5724         TCGA-CG-5725 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-CG-5726         TCGA-CG-5727         TCGA-CG-5728 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-CG-5730         TCGA-CG-5732         TCGA-CG-5733 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-CG-5734         TCGA-D7-5577         TCGA-D7-5578 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-D7-5579         TCGA-D7-6518         TCGA-D7-6519 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-D7-6520         TCGA-D7-6521         TCGA-D7-6522 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-D7-6524         TCGA-D7-6525         TCGA-D7-6526 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-D7-6527         TCGA-D7-6528         TCGA-D7-6815 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-D7-6817         TCGA-D7-6818         TCGA-D7-6820 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-D7-6822         TCGA-EQ-5647         TCGA-EQ-8122 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-F1-6177         TCGA-F1-6874         TCGA-F1-6875 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-FP-7735         TCGA-FP-7829         TCGA-FP-7916 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-FP-7998         TCGA-FP-8099         TCGA-FP-8209 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-FP-8210         TCGA-FP-8631         TCGA-HF-7131 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-HF-7132         TCGA-HF-7133         TCGA-HF-7134 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-HF-7136         TCGA-HJ-7597         TCGA-IN-7806 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-IN-7808         TCGA-IP-7968 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 

Clustering(38) Variable = 1p loss
D38V1, survival
                   sevent
clus2                 0   1
  1P LOSS CNV         7   2
  1P LOSS WILD-TYPE 117  17
      1P LOSS CNV 1P LOSS WILD-TYPE 
                9               134 
      1P LOSS CNV 1P LOSS WILD-TYPE 
                2                17 
$`1P LOSS CNV`
TCGA-BR-7959 TCGA-BR-A4PF TCGA-BR-A4QI TCGA-CG-4301 TCGA-CG-5724 TCGA-CG-5730 
        1.08         0.72         0.49         3.02        12.03         4.01 
TCGA-D7-6519 TCGA-D7-6526 TCGA-EQ-5647 
       15.65         6.61         0.62 

$`1P LOSS WILD-TYPE`
TCGA-B7-5816 TCGA-B7-5818 TCGA-BR-6452 TCGA-BR-6455 TCGA-BR-6457 TCGA-BR-6458 
        5.62         0.10         0.95         1.41         1.35         1.35 
TCGA-BR-6563 TCGA-BR-6564 TCGA-BR-6565 TCGA-BR-6566 TCGA-BR-6705 TCGA-BR-6706 
        0.85         0.82         0.62         0.62         1.71         2.17 
TCGA-BR-6707 TCGA-BR-6709 TCGA-BR-6710 TCGA-BR-6801 TCGA-BR-6802 TCGA-BR-6803 
        0.99         1.22         0.66         1.12         0.76         0.66 
TCGA-BR-6852 TCGA-BR-7196 TCGA-BR-7197 TCGA-BR-7703 TCGA-BR-7704 TCGA-BR-7707 
        0.26         1.22         1.48         0.46         1.25         0.13 
TCGA-BR-7715 TCGA-BR-7716 TCGA-BR-7717 TCGA-BR-7722 TCGA-BR-7723 TCGA-BR-7851 
        1.05         0.82         0.69         0.16         4.54         0.99 
TCGA-BR-7901 TCGA-BR-7957 TCGA-BR-7958 TCGA-BR-8059 TCGA-BR-8060 TCGA-BR-8077 
        0.95         0.69         0.16         0.82         1.32         0.69 
TCGA-BR-8078 TCGA-BR-8080 TCGA-BR-8081 TCGA-BR-8284 TCGA-BR-8285 TCGA-BR-8286 
        0.95         0.49         0.46         0.72         0.26         0.43 
TCGA-BR-8289 TCGA-BR-8291 TCGA-BR-8295 TCGA-BR-8296 TCGA-BR-8297 TCGA-BR-8592 
        0.26         1.18         1.55         1.48         0.76         0.20 
TCGA-BR-A4IU TCGA-BR-A4IV TCGA-BR-A4IY TCGA-BR-A4IZ TCGA-BR-A4J1 TCGA-BR-A4J2 
        0.59         0.92         0.39         0.79         0.72         0.79 
TCGA-BR-A4J4 TCGA-BR-A4J5 TCGA-BR-A4J6 TCGA-BR-A4J8 TCGA-BR-A4J9 TCGA-BR-A4QL 
        0.53         0.43         0.13         0.23         0.10         2.24 
TCGA-CD-5798 TCGA-CD-5799 TCGA-CD-5800 TCGA-CD-5801 TCGA-CD-5802 TCGA-CD-5803 
        0.82         0.69         0.36         0.49         0.30         0.07 
TCGA-CG-4300 TCGA-CG-4304 TCGA-CG-4305 TCGA-CG-4306 TCGA-CG-4436 TCGA-CG-4437 
       20.02        27.02        15.95         1.02        52.96         8.05 
TCGA-CG-4438 TCGA-CG-4440 TCGA-CG-4441 TCGA-CG-4443 TCGA-CG-4444 TCGA-CG-4449 
       54.05         4.01        14.01        29.98        47.05        19.07 
TCGA-CG-4455 TCGA-CG-4460 TCGA-CG-4462 TCGA-CG-4465 TCGA-CG-4466 TCGA-CG-4469 
       12.03        21.99         1.02         8.98        18.94         7.07 
TCGA-CG-4472 TCGA-CG-4474 TCGA-CG-4477 TCGA-CG-5716 TCGA-CG-5717 TCGA-CG-5718 
       12.00         1.02         1.02         1.02         6.94         1.02 
TCGA-CG-5719 TCGA-CG-5720 TCGA-CG-5721 TCGA-CG-5722 TCGA-CG-5723 TCGA-CG-5725 
        1.02         0.99         5.98         0.95        70.06        15.02 
TCGA-CG-5726 TCGA-CG-5727 TCGA-CG-5728 TCGA-CG-5732 TCGA-CG-5733 TCGA-CG-5734 
       28.96        31.04        65.10        55.04        21.07         7.99 
TCGA-D7-5577 TCGA-D7-5578 TCGA-D7-5579 TCGA-D7-6518 TCGA-D7-6520 TCGA-D7-6521 
        8.65         3.58         4.54         9.80         9.63         8.19 
TCGA-D7-6522 TCGA-D7-6524 TCGA-D7-6525 TCGA-D7-6527 TCGA-D7-6528 TCGA-D7-6815 
        6.90         0.69         5.95         4.14         1.68         3.65 
TCGA-D7-6817 TCGA-D7-6818 TCGA-D7-6820 TCGA-D7-6822 TCGA-EQ-8122 TCGA-F1-6177 
        4.70         4.04         2.93         4.27         7.79         6.54 
TCGA-F1-6874 TCGA-F1-6875 TCGA-FP-7735 TCGA-FP-7829 TCGA-FP-7916 TCGA-FP-7998 
        2.01        72.23         0.39         0.20         3.02         3.58 
TCGA-FP-8099 TCGA-FP-8209 TCGA-FP-8210 TCGA-FP-8631 TCGA-HJ-7597 TCGA-IN-7806 
        1.02        59.05         5.03         0.56        26.43         6.87 
TCGA-IN-7808 TCGA-IP-7968 
        3.55         2.53 

      1P LOSS CNV 1P LOSS WILD-TYPE 
             0.49              0.07 
      1P LOSS CNV 1P LOSS WILD-TYPE 
            15.65             72.23 
      1P LOSS CNV 1P LOSS WILD-TYPE 
            3.020             1.235 
[1] "0.5 - 15.7 (3.0)" "0.1 - 72.2 (1.2)"
       TCGA-B7-5816        TCGA-B7-5818        TCGA-BR-6452        TCGA-BR-6455 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-BR-6457        TCGA-BR-6458        TCGA-BR-6563        TCGA-BR-6564 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-BR-6565        TCGA-BR-6566        TCGA-BR-6705        TCGA-BR-6706 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-BR-6707        TCGA-BR-6709        TCGA-BR-6710        TCGA-BR-6801 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-BR-6802        TCGA-BR-6803        TCGA-BR-6852        TCGA-BR-7196 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-BR-7197        TCGA-BR-7703        TCGA-BR-7704        TCGA-BR-7707 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-BR-7715        TCGA-BR-7716        TCGA-BR-7717        TCGA-BR-7722 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-BR-7723        TCGA-BR-7851        TCGA-BR-7901        TCGA-BR-7957 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-BR-7958        TCGA-BR-7959        TCGA-BR-8059        TCGA-BR-8060 
"1P LOSS WILD-TYPE"       "1P LOSS CNV" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-BR-8077        TCGA-BR-8078        TCGA-BR-8080        TCGA-BR-8081 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-BR-8284        TCGA-BR-8285        TCGA-BR-8286        TCGA-BR-8289 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-BR-8291        TCGA-BR-8295        TCGA-BR-8296        TCGA-BR-8297 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-BR-8592        TCGA-BR-A4IU        TCGA-BR-A4IV        TCGA-BR-A4IY 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-BR-A4IZ        TCGA-BR-A4J1        TCGA-BR-A4J2        TCGA-BR-A4J4 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-BR-A4J5        TCGA-BR-A4J6        TCGA-BR-A4J8        TCGA-BR-A4J9 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-BR-A4PF        TCGA-BR-A4QI        TCGA-BR-A4QL        TCGA-CD-5798 
      "1P LOSS CNV"       "1P LOSS CNV" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-CD-5799        TCGA-CD-5800        TCGA-CD-5801        TCGA-CD-5802 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-CD-5803        TCGA-CG-4300        TCGA-CG-4301        TCGA-CG-4304 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE"       "1P LOSS CNV" "1P LOSS WILD-TYPE" 
       TCGA-CG-4305        TCGA-CG-4306        TCGA-CG-4436        TCGA-CG-4437 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-CG-4438        TCGA-CG-4440        TCGA-CG-4441        TCGA-CG-4443 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-CG-4444        TCGA-CG-4449        TCGA-CG-4455        TCGA-CG-4460 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-CG-4462        TCGA-CG-4465        TCGA-CG-4466        TCGA-CG-4469 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-CG-4472        TCGA-CG-4474        TCGA-CG-4477        TCGA-CG-5716 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-CG-5717        TCGA-CG-5718        TCGA-CG-5719        TCGA-CG-5720 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-CG-5721        TCGA-CG-5722        TCGA-CG-5723        TCGA-CG-5724 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE"       "1P LOSS CNV" 
       TCGA-CG-5725        TCGA-CG-5726        TCGA-CG-5727        TCGA-CG-5728 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-CG-5730        TCGA-CG-5732        TCGA-CG-5733        TCGA-CG-5734 
      "1P LOSS CNV" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-D7-5577        TCGA-D7-5578        TCGA-D7-5579        TCGA-D7-6518 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-D7-6519        TCGA-D7-6520        TCGA-D7-6521        TCGA-D7-6522 
      "1P LOSS CNV" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-D7-6524        TCGA-D7-6525        TCGA-D7-6526        TCGA-D7-6527 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE"       "1P LOSS CNV" "1P LOSS WILD-TYPE" 
       TCGA-D7-6528        TCGA-D7-6815        TCGA-D7-6817        TCGA-D7-6818 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-D7-6820        TCGA-D7-6822        TCGA-EQ-5647        TCGA-EQ-8122 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE"       "1P LOSS CNV" "1P LOSS WILD-TYPE" 
       TCGA-F1-6177        TCGA-F1-6874        TCGA-F1-6875        TCGA-FP-7735 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-FP-7829        TCGA-FP-7916        TCGA-FP-7998        TCGA-FP-8099 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-FP-8209        TCGA-FP-8210        TCGA-FP-8631        TCGA-HJ-7597 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-IN-7806        TCGA-IN-7808        TCGA-IP-7968 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-B7-5816        TCGA-B7-5818        TCGA-BR-6452        TCGA-BR-6455 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-BR-6457        TCGA-BR-6458        TCGA-BR-6563        TCGA-BR-6564 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-BR-6565        TCGA-BR-6566        TCGA-BR-6705        TCGA-BR-6706 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-BR-6707        TCGA-BR-6709        TCGA-BR-6710        TCGA-BR-6801 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-BR-6802        TCGA-BR-6803        TCGA-BR-6852        TCGA-BR-7196 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-BR-7197        TCGA-BR-7703        TCGA-BR-7704        TCGA-BR-7707 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-BR-7715        TCGA-BR-7716        TCGA-BR-7717        TCGA-BR-7722 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-BR-7723        TCGA-BR-7851        TCGA-BR-7901        TCGA-BR-7957 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-BR-7958        TCGA-BR-7959        TCGA-BR-8059        TCGA-BR-8060 
"1P LOSS WILD-TYPE"       "1P LOSS CNV" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-BR-8077        TCGA-BR-8078        TCGA-BR-8080        TCGA-BR-8081 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-BR-8284        TCGA-BR-8285        TCGA-BR-8286        TCGA-BR-8289 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-BR-8291        TCGA-BR-8295        TCGA-BR-8296        TCGA-BR-8297 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-BR-8592        TCGA-BR-A4IU        TCGA-BR-A4IV        TCGA-BR-A4IY 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-BR-A4IZ        TCGA-BR-A4J1        TCGA-BR-A4J2        TCGA-BR-A4J4 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-BR-A4J5        TCGA-BR-A4J6        TCGA-BR-A4J8        TCGA-BR-A4J9 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-BR-A4PF        TCGA-BR-A4QI        TCGA-BR-A4QL        TCGA-CD-5798 
      "1P LOSS CNV"       "1P LOSS CNV" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-CD-5799        TCGA-CD-5800        TCGA-CD-5801        TCGA-CD-5802 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-CD-5803        TCGA-CG-4300        TCGA-CG-4301        TCGA-CG-4304 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE"       "1P LOSS CNV" "1P LOSS WILD-TYPE" 
       TCGA-CG-4305        TCGA-CG-4306        TCGA-CG-4436        TCGA-CG-4437 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-CG-4438        TCGA-CG-4440        TCGA-CG-4441        TCGA-CG-4443 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-CG-4444        TCGA-CG-4449        TCGA-CG-4455        TCGA-CG-4460 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-CG-4462        TCGA-CG-4465        TCGA-CG-4466        TCGA-CG-4469 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-CG-4472        TCGA-CG-4474        TCGA-CG-4477        TCGA-CG-5716 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-CG-5717        TCGA-CG-5718        TCGA-CG-5719        TCGA-CG-5720 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-CG-5721        TCGA-CG-5722        TCGA-CG-5723        TCGA-CG-5724 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE"       "1P LOSS CNV" 
       TCGA-CG-5725        TCGA-CG-5726        TCGA-CG-5727        TCGA-CG-5728 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-CG-5730        TCGA-CG-5732        TCGA-CG-5733        TCGA-CG-5734 
      "1P LOSS CNV" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-D7-5577        TCGA-D7-5578        TCGA-D7-5579        TCGA-D7-6518 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-D7-6519        TCGA-D7-6520        TCGA-D7-6521        TCGA-D7-6522 
      "1P LOSS CNV" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-D7-6524        TCGA-D7-6525        TCGA-D7-6526        TCGA-D7-6527 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE"       "1P LOSS CNV" "1P LOSS WILD-TYPE" 
       TCGA-D7-6528        TCGA-D7-6815        TCGA-D7-6817        TCGA-D7-6818 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-D7-6820        TCGA-D7-6822        TCGA-EQ-5647        TCGA-EQ-8122 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE"       "1P LOSS CNV" "1P LOSS WILD-TYPE" 
       TCGA-F1-6177        TCGA-F1-6874        TCGA-F1-6875        TCGA-FP-7735 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-FP-7829        TCGA-FP-7916        TCGA-FP-7998        TCGA-FP-8099 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-FP-8209        TCGA-FP-8210        TCGA-FP-8631        TCGA-HJ-7597 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-IN-7806        TCGA-IN-7808        TCGA-IP-7968 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-B7-5816        TCGA-B7-5818        TCGA-BR-6452        TCGA-BR-6455 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-BR-6457        TCGA-BR-6458        TCGA-BR-6563        TCGA-BR-6564 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-BR-6565        TCGA-BR-6566        TCGA-BR-6705        TCGA-BR-6706 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-BR-6707        TCGA-BR-6709        TCGA-BR-6710        TCGA-BR-6801 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-BR-6802        TCGA-BR-6803        TCGA-BR-6852        TCGA-BR-7196 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-BR-7197        TCGA-BR-7703        TCGA-BR-7704        TCGA-BR-7707 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-BR-7715        TCGA-BR-7716        TCGA-BR-7717        TCGA-BR-7722 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-BR-7723        TCGA-BR-7851        TCGA-BR-7901        TCGA-BR-7957 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-BR-7958        TCGA-BR-7959        TCGA-BR-8059        TCGA-BR-8060 
"1P LOSS WILD-TYPE"       "1P LOSS CNV" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-BR-8077        TCGA-BR-8078        TCGA-BR-8080        TCGA-BR-8081 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-BR-8284        TCGA-BR-8285        TCGA-BR-8286        TCGA-BR-8289 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-BR-8291        TCGA-BR-8295        TCGA-BR-8296        TCGA-BR-8297 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-BR-8592        TCGA-BR-A4IU        TCGA-BR-A4IV        TCGA-BR-A4IY 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-BR-A4IZ        TCGA-BR-A4J1        TCGA-BR-A4J2        TCGA-BR-A4J4 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-BR-A4J5        TCGA-BR-A4J6        TCGA-BR-A4J8        TCGA-BR-A4J9 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-BR-A4PF        TCGA-BR-A4QI        TCGA-BR-A4QL        TCGA-CD-5798 
      "1P LOSS CNV"       "1P LOSS CNV" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-CD-5799        TCGA-CD-5800        TCGA-CD-5801        TCGA-CD-5802 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-CD-5803        TCGA-CG-4300        TCGA-CG-4301        TCGA-CG-4304 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE"       "1P LOSS CNV" "1P LOSS WILD-TYPE" 
       TCGA-CG-4305        TCGA-CG-4306        TCGA-CG-4436        TCGA-CG-4437 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-CG-4438        TCGA-CG-4440        TCGA-CG-4441        TCGA-CG-4443 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-CG-4444        TCGA-CG-4449        TCGA-CG-4455        TCGA-CG-4460 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-CG-4462        TCGA-CG-4465        TCGA-CG-4466        TCGA-CG-4469 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-CG-4472        TCGA-CG-4474        TCGA-CG-4477        TCGA-CG-5716 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-CG-5717        TCGA-CG-5718        TCGA-CG-5719        TCGA-CG-5720 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-CG-5721        TCGA-CG-5722        TCGA-CG-5723        TCGA-CG-5724 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE"       "1P LOSS CNV" 
       TCGA-CG-5725        TCGA-CG-5726        TCGA-CG-5727        TCGA-CG-5728 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-CG-5730        TCGA-CG-5732        TCGA-CG-5733        TCGA-CG-5734 
      "1P LOSS CNV" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-D7-5577        TCGA-D7-5578        TCGA-D7-5579        TCGA-D7-6518 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-D7-6519        TCGA-D7-6520        TCGA-D7-6521        TCGA-D7-6522 
      "1P LOSS CNV" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-D7-6524        TCGA-D7-6525        TCGA-D7-6526        TCGA-D7-6527 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE"       "1P LOSS CNV" "1P LOSS WILD-TYPE" 
       TCGA-D7-6528        TCGA-D7-6815        TCGA-D7-6817        TCGA-D7-6818 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-D7-6820        TCGA-D7-6822        TCGA-EQ-5647        TCGA-EQ-8122 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE"       "1P LOSS CNV" "1P LOSS WILD-TYPE" 
       TCGA-F1-6177        TCGA-F1-6874        TCGA-F1-6875        TCGA-FP-7735 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-FP-7829        TCGA-FP-7916        TCGA-FP-7998        TCGA-FP-8099 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-FP-8209        TCGA-FP-8210        TCGA-FP-8631        TCGA-HJ-7597 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-IN-7806        TCGA-IN-7808        TCGA-IP-7968 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
[1] "hr=" "2.6"
D38V2, continuous
D38V3, binary
[1] "tbl2"
                   cls
clus                [,1] [,2]
  1P LOSS CNV          6    4
  1P LOSS WILD-TYPE   66  104
        clus
vv       1P LOSS CNV 1P LOSS WILD-TYPE
  FEMALE           6                66
  MALE             4               104
                   vv
clus                STOMACH  ADENOCARCINOMA  DIFFUSE TYPE
  1P LOSS CNV                                           0
  1P LOSS WILD-TYPE                                    10
                   vv
clus                STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  1P LOSS CNV                                                            2
  1P LOSS WILD-TYPE                                                     14
                   vv
clus                STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  1P LOSS CNV                                                                       0
  1P LOSS WILD-TYPE                                                                 8
                   vv
clus                STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE
  1P LOSS CNV                                                              1
  1P LOSS WILD-TYPE                                                        2
                   vv
clus                STOMACH ADENOCARCINOMA  SIGNET RING TYPE
  1P LOSS CNV                                              0
  1P LOSS WILD-TYPE                                        1
                   vv
clus                STOMACH ADENOCARCINOMA - DIFFUSE TYPE
  1P LOSS CNV                                           2
  1P LOSS WILD-TYPE                                    14
                   vv
clus                STOMACH ADENOCARCINOMA - NOT OTHERWISE SPECIFIED (NOS)
  1P LOSS CNV                                                            2
  1P LOSS WILD-TYPE                                                     71
                   vv
clus                STOMACH INTESTINAL ADENOCARCINOMA - MUCINOUS TYPE
  1P LOSS CNV                                                       0
  1P LOSS WILD-TYPE                                                 7
                   vv
clus                STOMACH INTESTINAL ADENOCARCINOMA - PAPILLARY TYPE
  1P LOSS CNV                                                        0
  1P LOSS WILD-TYPE                                                  3
                   vv
clus                STOMACH INTESTINAL ADENOCARCINOMA - TUBULAR TYPE
  1P LOSS CNV                                                      2
  1P LOSS WILD-TYPE                                                8
                   vv
clus                STOMACH INTESTINAL ADENOCARCINOMA - TYPE NOT OTHERWISE SPECIFIED (NOS)
  1P LOSS CNV                                                                            1
  1P LOSS WILD-TYPE                                                                     27
D38V4, multiclass
                   vv
clus                T1 T2 T3 T4
  1P LOSS CNV        0  3  2  2
  1P LOSS WILD-TYPE  6 49 54 16
D38V5, multiclass
    clus
vv   1P LOSS CNV 1P LOSS WILD-TYPE
  T1           0                 6
  T2           3                49
  T3           2                54
  T4           2                16
                   vv
clus                N0 N1 N2 N3
  1P LOSS CNV        0  3  1  2
  1P LOSS WILD-TYPE 44 46 22 13
D38V6, multiclass
    clus
vv   1P LOSS CNV 1P LOSS WILD-TYPE
  N0           0                44
  N1           3                46
  N2           1                22
  N3           2                13
                   vv
clus                 M0  M1  MX
  1P LOSS CNV         3   4   0
  1P LOSS WILD-TYPE 115  12   8
D38V7, multiclass
    clus
vv   1P LOSS CNV 1P LOSS WILD-TYPE
  M0           3               115
  M1           4                12
  MX           0                 8
                   vv
clus                 I II III IV
  1P LOSS CNV        0  0   2  4
  1P LOSS WILD-TYPE 24 37  37 22
D38V8, multiclass
     clus
vv    1P LOSS CNV 1P LOSS WILD-TYPE
  I             0                24
  II            0                37
  III           2                37
  IV            4                22
D38V9, binary
[1] "tbl2"
                   cls
clus                [,1] [,2]
  1P LOSS CNV          0   10
  1P LOSS WILD-TYPE    5  165
     clus
vv    1P LOSS CNV 1P LOSS WILD-TYPE
  NO            0                 5
  YES          10               165
                   vv
clus                 R0  R1  R2  RX
  1P LOSS CNV         5   0   4   1
  1P LOSS WILD-TYPE 120   7   8  24
D38V10, multiclass
    clus
vv   1P LOSS CNV 1P LOSS WILD-TYPE
  R0           5               120
  R1           0                 7
  R2           4                 8
  RX           1                24
D38V11, continuous

Clustering(39) Variable = 2p loss
D39V1, survival
                   sevent
clus2                 0   1
  2P LOSS CNV         1   0
  2P LOSS WILD-TYPE 123  19
      2P LOSS CNV 2P LOSS WILD-TYPE 
                1               142 
      2P LOSS CNV 2P LOSS WILD-TYPE 
                0                19 
$`2P LOSS CNV`
TCGA-BR-8060 
        1.32 

$`2P LOSS WILD-TYPE`
TCGA-B7-5816 TCGA-B7-5818 TCGA-BR-6452 TCGA-BR-6455 TCGA-BR-6457 TCGA-BR-6458 
        5.62         0.10         0.95         1.41         1.35         1.35 
TCGA-BR-6563 TCGA-BR-6564 TCGA-BR-6565 TCGA-BR-6566 TCGA-BR-6705 TCGA-BR-6706 
        0.85         0.82         0.62         0.62         1.71         2.17 
TCGA-BR-6707 TCGA-BR-6709 TCGA-BR-6710 TCGA-BR-6801 TCGA-BR-6802 TCGA-BR-6803 
        0.99         1.22         0.66         1.12         0.76         0.66 
TCGA-BR-6852 TCGA-BR-7196 TCGA-BR-7197 TCGA-BR-7703 TCGA-BR-7704 TCGA-BR-7707 
        0.26         1.22         1.48         0.46         1.25         0.13 
TCGA-BR-7715 TCGA-BR-7716 TCGA-BR-7717 TCGA-BR-7722 TCGA-BR-7723 TCGA-BR-7851 
        1.05         0.82         0.69         0.16         4.54         0.99 
TCGA-BR-7901 TCGA-BR-7957 TCGA-BR-7958 TCGA-BR-7959 TCGA-BR-8059 TCGA-BR-8077 
        0.95         0.69         0.16         1.08         0.82         0.69 
TCGA-BR-8078 TCGA-BR-8080 TCGA-BR-8081 TCGA-BR-8284 TCGA-BR-8285 TCGA-BR-8286 
        0.95         0.49         0.46         0.72         0.26         0.43 
TCGA-BR-8289 TCGA-BR-8291 TCGA-BR-8295 TCGA-BR-8296 TCGA-BR-8297 TCGA-BR-8592 
        0.26         1.18         1.55         1.48         0.76         0.20 
TCGA-BR-A4IU TCGA-BR-A4IV TCGA-BR-A4IY TCGA-BR-A4IZ TCGA-BR-A4J1 TCGA-BR-A4J2 
        0.59         0.92         0.39         0.79         0.72         0.79 
TCGA-BR-A4J4 TCGA-BR-A4J5 TCGA-BR-A4J6 TCGA-BR-A4J8 TCGA-BR-A4J9 TCGA-BR-A4PF 
        0.53         0.43         0.13         0.23         0.10         0.72 
TCGA-BR-A4QI TCGA-BR-A4QL TCGA-CD-5798 TCGA-CD-5799 TCGA-CD-5800 TCGA-CD-5801 
        0.49         2.24         0.82         0.69         0.36         0.49 
TCGA-CD-5802 TCGA-CD-5803 TCGA-CG-4300 TCGA-CG-4301 TCGA-CG-4304 TCGA-CG-4305 
        0.30         0.07        20.02         3.02        27.02        15.95 
TCGA-CG-4306 TCGA-CG-4436 TCGA-CG-4437 TCGA-CG-4438 TCGA-CG-4440 TCGA-CG-4441 
        1.02        52.96         8.05        54.05         4.01        14.01 
TCGA-CG-4443 TCGA-CG-4444 TCGA-CG-4449 TCGA-CG-4455 TCGA-CG-4460 TCGA-CG-4462 
       29.98        47.05        19.07        12.03        21.99         1.02 
TCGA-CG-4465 TCGA-CG-4466 TCGA-CG-4469 TCGA-CG-4472 TCGA-CG-4474 TCGA-CG-4477 
        8.98        18.94         7.07        12.00         1.02         1.02 
TCGA-CG-5716 TCGA-CG-5717 TCGA-CG-5718 TCGA-CG-5719 TCGA-CG-5720 TCGA-CG-5721 
        1.02         6.94         1.02         1.02         0.99         5.98 
TCGA-CG-5722 TCGA-CG-5723 TCGA-CG-5724 TCGA-CG-5725 TCGA-CG-5726 TCGA-CG-5727 
        0.95        70.06        12.03        15.02        28.96        31.04 
TCGA-CG-5728 TCGA-CG-5730 TCGA-CG-5732 TCGA-CG-5733 TCGA-CG-5734 TCGA-D7-5577 
       65.10         4.01        55.04        21.07         7.99         8.65 
TCGA-D7-5578 TCGA-D7-5579 TCGA-D7-6518 TCGA-D7-6519 TCGA-D7-6520 TCGA-D7-6521 
        3.58         4.54         9.80        15.65         9.63         8.19 
TCGA-D7-6522 TCGA-D7-6524 TCGA-D7-6525 TCGA-D7-6526 TCGA-D7-6527 TCGA-D7-6528 
        6.90         0.69         5.95         6.61         4.14         1.68 
TCGA-D7-6815 TCGA-D7-6817 TCGA-D7-6818 TCGA-D7-6820 TCGA-D7-6822 TCGA-EQ-5647 
        3.65         4.70         4.04         2.93         4.27         0.62 
TCGA-EQ-8122 TCGA-F1-6177 TCGA-F1-6874 TCGA-F1-6875 TCGA-FP-7735 TCGA-FP-7829 
        7.79         6.54         2.01        72.23         0.39         0.20 
TCGA-FP-7916 TCGA-FP-7998 TCGA-FP-8099 TCGA-FP-8209 TCGA-FP-8210 TCGA-FP-8631 
        3.02         3.58         1.02        59.05         5.03         0.56 
TCGA-HJ-7597 TCGA-IN-7806 TCGA-IN-7808 TCGA-IP-7968 
       26.43         6.87         3.55         2.53 

      2P LOSS CNV 2P LOSS WILD-TYPE 
             1.32              0.07 
      2P LOSS CNV 2P LOSS WILD-TYPE 
             1.32             72.23 
      2P LOSS CNV 2P LOSS WILD-TYPE 
            1.320             1.235 
[1] "1.3 - 1.3 (1.3)"  "0.1 - 72.2 (1.2)"
       TCGA-B7-5816        TCGA-B7-5818        TCGA-BR-6452        TCGA-BR-6455 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-BR-6457        TCGA-BR-6458        TCGA-BR-6563        TCGA-BR-6564 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-BR-6565        TCGA-BR-6566        TCGA-BR-6705        TCGA-BR-6706 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-BR-6707        TCGA-BR-6709        TCGA-BR-6710        TCGA-BR-6801 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-BR-6802        TCGA-BR-6803        TCGA-BR-6852        TCGA-BR-7196 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-BR-7197        TCGA-BR-7703        TCGA-BR-7704        TCGA-BR-7707 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-BR-7715        TCGA-BR-7716        TCGA-BR-7717        TCGA-BR-7722 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-BR-7723        TCGA-BR-7851        TCGA-BR-7901        TCGA-BR-7957 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-BR-7958        TCGA-BR-7959        TCGA-BR-8059        TCGA-BR-8060 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE"       "2P LOSS CNV" 
       TCGA-BR-8077        TCGA-BR-8078        TCGA-BR-8080        TCGA-BR-8081 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-BR-8284        TCGA-BR-8285        TCGA-BR-8286        TCGA-BR-8289 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-BR-8291        TCGA-BR-8295        TCGA-BR-8296        TCGA-BR-8297 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-BR-8592        TCGA-BR-A4IU        TCGA-BR-A4IV        TCGA-BR-A4IY 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-BR-A4IZ        TCGA-BR-A4J1        TCGA-BR-A4J2        TCGA-BR-A4J4 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-BR-A4J5        TCGA-BR-A4J6        TCGA-BR-A4J8        TCGA-BR-A4J9 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-BR-A4PF        TCGA-BR-A4QI        TCGA-BR-A4QL        TCGA-CD-5798 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-CD-5799        TCGA-CD-5800        TCGA-CD-5801        TCGA-CD-5802 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-CD-5803        TCGA-CG-4300        TCGA-CG-4301        TCGA-CG-4304 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-CG-4305        TCGA-CG-4306        TCGA-CG-4436        TCGA-CG-4437 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-CG-4438        TCGA-CG-4440        TCGA-CG-4441        TCGA-CG-4443 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-CG-4444        TCGA-CG-4449        TCGA-CG-4455        TCGA-CG-4460 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-CG-4462        TCGA-CG-4465        TCGA-CG-4466        TCGA-CG-4469 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-CG-4472        TCGA-CG-4474        TCGA-CG-4477        TCGA-CG-5716 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-CG-5717        TCGA-CG-5718        TCGA-CG-5719        TCGA-CG-5720 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-CG-5721        TCGA-CG-5722        TCGA-CG-5723        TCGA-CG-5724 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-CG-5725        TCGA-CG-5726        TCGA-CG-5727        TCGA-CG-5728 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-CG-5730        TCGA-CG-5732        TCGA-CG-5733        TCGA-CG-5734 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-D7-5577        TCGA-D7-5578        TCGA-D7-5579        TCGA-D7-6518 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-D7-6519        TCGA-D7-6520        TCGA-D7-6521        TCGA-D7-6522 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-D7-6524        TCGA-D7-6525        TCGA-D7-6526        TCGA-D7-6527 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-D7-6528        TCGA-D7-6815        TCGA-D7-6817        TCGA-D7-6818 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-D7-6820        TCGA-D7-6822        TCGA-EQ-5647        TCGA-EQ-8122 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-F1-6177        TCGA-F1-6874        TCGA-F1-6875        TCGA-FP-7735 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-FP-7829        TCGA-FP-7916        TCGA-FP-7998        TCGA-FP-8099 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-FP-8209        TCGA-FP-8210        TCGA-FP-8631        TCGA-HJ-7597 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-IN-7806        TCGA-IN-7808        TCGA-IP-7968 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-B7-5816        TCGA-B7-5818        TCGA-BR-6452        TCGA-BR-6455 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-BR-6457        TCGA-BR-6458        TCGA-BR-6563        TCGA-BR-6564 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-BR-6565        TCGA-BR-6566        TCGA-BR-6705        TCGA-BR-6706 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-BR-6707        TCGA-BR-6709        TCGA-BR-6710        TCGA-BR-6801 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-BR-6802        TCGA-BR-6803        TCGA-BR-6852        TCGA-BR-7196 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-BR-7197        TCGA-BR-7703        TCGA-BR-7704        TCGA-BR-7707 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-BR-7715        TCGA-BR-7716        TCGA-BR-7717        TCGA-BR-7722 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-BR-7723        TCGA-BR-7851        TCGA-BR-7901        TCGA-BR-7957 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-BR-7958        TCGA-BR-7959        TCGA-BR-8059        TCGA-BR-8060 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE"       "2P LOSS CNV" 
       TCGA-BR-8077        TCGA-BR-8078        TCGA-BR-8080        TCGA-BR-8081 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-BR-8284        TCGA-BR-8285        TCGA-BR-8286        TCGA-BR-8289 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-BR-8291        TCGA-BR-8295        TCGA-BR-8296        TCGA-BR-8297 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-BR-8592        TCGA-BR-A4IU        TCGA-BR-A4IV        TCGA-BR-A4IY 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-BR-A4IZ        TCGA-BR-A4J1        TCGA-BR-A4J2        TCGA-BR-A4J4 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-BR-A4J5        TCGA-BR-A4J6        TCGA-BR-A4J8        TCGA-BR-A4J9 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-BR-A4PF        TCGA-BR-A4QI        TCGA-BR-A4QL        TCGA-CD-5798 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-CD-5799        TCGA-CD-5800        TCGA-CD-5801        TCGA-CD-5802 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-CD-5803        TCGA-CG-4300        TCGA-CG-4301        TCGA-CG-4304 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-CG-4305        TCGA-CG-4306        TCGA-CG-4436        TCGA-CG-4437 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-CG-4438        TCGA-CG-4440        TCGA-CG-4441        TCGA-CG-4443 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-CG-4444        TCGA-CG-4449        TCGA-CG-4455        TCGA-CG-4460 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-CG-4462        TCGA-CG-4465        TCGA-CG-4466        TCGA-CG-4469 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-CG-4472        TCGA-CG-4474        TCGA-CG-4477        TCGA-CG-5716 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-CG-5717        TCGA-CG-5718        TCGA-CG-5719        TCGA-CG-5720 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-CG-5721        TCGA-CG-5722        TCGA-CG-5723        TCGA-CG-5724 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-CG-5725        TCGA-CG-5726        TCGA-CG-5727        TCGA-CG-5728 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-CG-5730        TCGA-CG-5732        TCGA-CG-5733        TCGA-CG-5734 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-D7-5577        TCGA-D7-5578        TCGA-D7-5579        TCGA-D7-6518 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-D7-6519        TCGA-D7-6520        TCGA-D7-6521        TCGA-D7-6522 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-D7-6524        TCGA-D7-6525        TCGA-D7-6526        TCGA-D7-6527 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-D7-6528        TCGA-D7-6815        TCGA-D7-6817        TCGA-D7-6818 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-D7-6820        TCGA-D7-6822        TCGA-EQ-5647        TCGA-EQ-8122 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-F1-6177        TCGA-F1-6874        TCGA-F1-6875        TCGA-FP-7735 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-FP-7829        TCGA-FP-7916        TCGA-FP-7998        TCGA-FP-8099 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-FP-8209        TCGA-FP-8210        TCGA-FP-8631        TCGA-HJ-7597 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-IN-7806        TCGA-IN-7808        TCGA-IP-7968 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-B7-5816        TCGA-B7-5818        TCGA-BR-6452        TCGA-BR-6455 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-BR-6457        TCGA-BR-6458        TCGA-BR-6563        TCGA-BR-6564 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-BR-6565        TCGA-BR-6566        TCGA-BR-6705        TCGA-BR-6706 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-BR-6707        TCGA-BR-6709        TCGA-BR-6710        TCGA-BR-6801 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-BR-6802        TCGA-BR-6803        TCGA-BR-6852        TCGA-BR-7196 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-BR-7197        TCGA-BR-7703        TCGA-BR-7704        TCGA-BR-7707 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-BR-7715        TCGA-BR-7716        TCGA-BR-7717        TCGA-BR-7722 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-BR-7723        TCGA-BR-7851        TCGA-BR-7901        TCGA-BR-7957 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-BR-7958        TCGA-BR-7959        TCGA-BR-8059        TCGA-BR-8060 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE"       "2P LOSS CNV" 
       TCGA-BR-8077        TCGA-BR-8078        TCGA-BR-8080        TCGA-BR-8081 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-BR-8284        TCGA-BR-8285        TCGA-BR-8286        TCGA-BR-8289 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-BR-8291        TCGA-BR-8295        TCGA-BR-8296        TCGA-BR-8297 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-BR-8592        TCGA-BR-A4IU        TCGA-BR-A4IV        TCGA-BR-A4IY 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-BR-A4IZ        TCGA-BR-A4J1        TCGA-BR-A4J2        TCGA-BR-A4J4 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-BR-A4J5        TCGA-BR-A4J6        TCGA-BR-A4J8        TCGA-BR-A4J9 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-BR-A4PF        TCGA-BR-A4QI        TCGA-BR-A4QL        TCGA-CD-5798 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-CD-5799        TCGA-CD-5800        TCGA-CD-5801        TCGA-CD-5802 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-CD-5803        TCGA-CG-4300        TCGA-CG-4301        TCGA-CG-4304 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-CG-4305        TCGA-CG-4306        TCGA-CG-4436        TCGA-CG-4437 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-CG-4438        TCGA-CG-4440        TCGA-CG-4441        TCGA-CG-4443 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-CG-4444        TCGA-CG-4449        TCGA-CG-4455        TCGA-CG-4460 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-CG-4462        TCGA-CG-4465        TCGA-CG-4466        TCGA-CG-4469 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-CG-4472        TCGA-CG-4474        TCGA-CG-4477        TCGA-CG-5716 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-CG-5717        TCGA-CG-5718        TCGA-CG-5719        TCGA-CG-5720 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-CG-5721        TCGA-CG-5722        TCGA-CG-5723        TCGA-CG-5724 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-CG-5725        TCGA-CG-5726        TCGA-CG-5727        TCGA-CG-5728 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-CG-5730        TCGA-CG-5732        TCGA-CG-5733        TCGA-CG-5734 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-D7-5577        TCGA-D7-5578        TCGA-D7-5579        TCGA-D7-6518 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-D7-6519        TCGA-D7-6520        TCGA-D7-6521        TCGA-D7-6522 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-D7-6524        TCGA-D7-6525        TCGA-D7-6526        TCGA-D7-6527 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-D7-6528        TCGA-D7-6815        TCGA-D7-6817        TCGA-D7-6818 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-D7-6820        TCGA-D7-6822        TCGA-EQ-5647        TCGA-EQ-8122 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-F1-6177        TCGA-F1-6874        TCGA-F1-6875        TCGA-FP-7735 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-FP-7829        TCGA-FP-7916        TCGA-FP-7998        TCGA-FP-8099 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-FP-8209        TCGA-FP-8210        TCGA-FP-8631        TCGA-HJ-7597 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-IN-7806        TCGA-IN-7808        TCGA-IP-7968 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
[1] "Remove cluster labels:" "2P LOSS CNV"           
clus
      2P LOSS CNV 2P LOSS WILD-TYPE 
                1               142 
       TCGA-B7-5816        TCGA-B7-5818        TCGA-BR-6452        TCGA-BR-6455 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-BR-6457        TCGA-BR-6458        TCGA-BR-6563        TCGA-BR-6564 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-BR-6565        TCGA-BR-6566        TCGA-BR-6705        TCGA-BR-6706 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-BR-6707        TCGA-BR-6709        TCGA-BR-6710        TCGA-BR-6801 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-BR-6802        TCGA-BR-6803        TCGA-BR-6852        TCGA-BR-7196 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-BR-7197        TCGA-BR-7703        TCGA-BR-7704        TCGA-BR-7707 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-BR-7715        TCGA-BR-7716        TCGA-BR-7717        TCGA-BR-7722 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-BR-7723        TCGA-BR-7851        TCGA-BR-7901        TCGA-BR-7957 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-BR-7958        TCGA-BR-7959        TCGA-BR-8059        TCGA-BR-8077 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-BR-8078        TCGA-BR-8080        TCGA-BR-8081        TCGA-BR-8284 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-BR-8285        TCGA-BR-8286        TCGA-BR-8289        TCGA-BR-8291 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-BR-8295        TCGA-BR-8296        TCGA-BR-8297        TCGA-BR-8592 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-BR-A4IU        TCGA-BR-A4IV        TCGA-BR-A4IY        TCGA-BR-A4IZ 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-BR-A4J1        TCGA-BR-A4J2        TCGA-BR-A4J4        TCGA-BR-A4J5 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-BR-A4J6        TCGA-BR-A4J8        TCGA-BR-A4J9        TCGA-BR-A4PF 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-BR-A4QI        TCGA-BR-A4QL        TCGA-CD-5798        TCGA-CD-5799 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-CD-5800        TCGA-CD-5801        TCGA-CD-5802        TCGA-CD-5803 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-CG-4300        TCGA-CG-4301        TCGA-CG-4304        TCGA-CG-4305 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-CG-4306        TCGA-CG-4436        TCGA-CG-4437        TCGA-CG-4438 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-CG-4440        TCGA-CG-4441        TCGA-CG-4443        TCGA-CG-4444 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-CG-4449        TCGA-CG-4455        TCGA-CG-4460        TCGA-CG-4462 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-CG-4465        TCGA-CG-4466        TCGA-CG-4469        TCGA-CG-4472 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-CG-4474        TCGA-CG-4477        TCGA-CG-5716        TCGA-CG-5717 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-CG-5718        TCGA-CG-5719        TCGA-CG-5720        TCGA-CG-5721 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-CG-5722        TCGA-CG-5723        TCGA-CG-5724        TCGA-CG-5725 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-CG-5726        TCGA-CG-5727        TCGA-CG-5728        TCGA-CG-5730 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-CG-5732        TCGA-CG-5733        TCGA-CG-5734        TCGA-D7-5577 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-D7-5578        TCGA-D7-5579        TCGA-D7-6518        TCGA-D7-6519 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-D7-6520        TCGA-D7-6521        TCGA-D7-6522        TCGA-D7-6524 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-D7-6525        TCGA-D7-6526        TCGA-D7-6527        TCGA-D7-6528 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-D7-6815        TCGA-D7-6817        TCGA-D7-6818        TCGA-D7-6820 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-D7-6822        TCGA-EQ-5647        TCGA-EQ-8122        TCGA-F1-6177 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-F1-6874        TCGA-F1-6875        TCGA-FP-7735        TCGA-FP-7829 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-FP-7916        TCGA-FP-7998        TCGA-FP-8099        TCGA-FP-8209 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-FP-8210        TCGA-FP-8631        TCGA-HJ-7597        TCGA-IN-7806 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-IN-7808        TCGA-IP-7968 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
D39V2, continuous
[1] "Remove cluster labels:" "2P LOSS CNV"           
clus
      2P LOSS CNV 2P LOSS WILD-TYPE 
                2               171 
       TCGA-B7-5816        TCGA-B7-5818        TCGA-BR-4183        TCGA-BR-4184 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-BR-4187        TCGA-BR-4188        TCGA-BR-4191        TCGA-BR-4201 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-BR-4253        TCGA-BR-4255        TCGA-BR-4256        TCGA-BR-4257 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-BR-4267        TCGA-BR-4279        TCGA-BR-4280        TCGA-BR-4292 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-BR-4294        TCGA-BR-4357        TCGA-BR-4361        TCGA-BR-4362 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-BR-4363        TCGA-BR-4366        TCGA-BR-4367        TCGA-BR-4368 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-BR-4369        TCGA-BR-4370        TCGA-BR-4371        TCGA-BR-6452 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-BR-6453        TCGA-BR-6454        TCGA-BR-6455        TCGA-BR-6456 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-BR-6457        TCGA-BR-6458        TCGA-BR-6563        TCGA-BR-6564 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-BR-6565        TCGA-BR-6566        TCGA-BR-6705        TCGA-BR-6706 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-BR-6707        TCGA-BR-6709        TCGA-BR-6710        TCGA-BR-6801 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-BR-6802        TCGA-BR-6803        TCGA-BR-6852        TCGA-BR-7196 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-BR-7197        TCGA-BR-7703        TCGA-BR-7704        TCGA-BR-7707 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-BR-7715        TCGA-BR-7716        TCGA-BR-7717        TCGA-BR-7722 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-BR-7723        TCGA-BR-7851        TCGA-BR-7901        TCGA-BR-7957 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-BR-7958        TCGA-BR-7959        TCGA-BR-8059        TCGA-BR-8077 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-BR-8078        TCGA-BR-8080        TCGA-BR-8081        TCGA-BR-8284 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-BR-8285        TCGA-BR-8286        TCGA-BR-8289        TCGA-BR-8291 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-BR-8295        TCGA-BR-8296        TCGA-BR-8297        TCGA-BR-8592 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-BR-A4IU        TCGA-BR-A4IV        TCGA-BR-A4IY        TCGA-BR-A4IZ 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-BR-A4J1        TCGA-BR-A4J2        TCGA-BR-A4J4        TCGA-BR-A4J5 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-BR-A4J6        TCGA-BR-A4J8        TCGA-BR-A4J9        TCGA-BR-A4PF 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-BR-A4QI        TCGA-BR-A4QL        TCGA-CD-5798        TCGA-CD-5799 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-CD-5802        TCGA-CD-5803        TCGA-CD-5804        TCGA-CG-4300 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-CG-4301        TCGA-CG-4304        TCGA-CG-4305        TCGA-CG-4306 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-CG-4436        TCGA-CG-4437        TCGA-CG-4438        TCGA-CG-4440 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-CG-4441        TCGA-CG-4442        TCGA-CG-4443        TCGA-CG-4444 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-CG-4449        TCGA-CG-4455        TCGA-CG-4460        TCGA-CG-4462 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-CG-4465        TCGA-CG-4466        TCGA-CG-4469        TCGA-CG-4472 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-CG-4474        TCGA-CG-4476        TCGA-CG-4477        TCGA-CG-5716 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-CG-5717        TCGA-CG-5718        TCGA-CG-5719        TCGA-CG-5720 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-CG-5721        TCGA-CG-5722        TCGA-CG-5723        TCGA-CG-5724 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-CG-5725        TCGA-CG-5726        TCGA-CG-5727        TCGA-CG-5728 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-CG-5730        TCGA-CG-5732        TCGA-CG-5733        TCGA-CG-5734 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-D7-5577        TCGA-D7-5578        TCGA-D7-5579        TCGA-D7-6518 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-D7-6519        TCGA-D7-6520        TCGA-D7-6521        TCGA-D7-6522 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-D7-6524        TCGA-D7-6525        TCGA-D7-6526        TCGA-D7-6527 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-D7-6528        TCGA-D7-6815        TCGA-D7-6817        TCGA-D7-6818 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-D7-6820        TCGA-D7-6822        TCGA-EQ-5647        TCGA-EQ-8122 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-F1-6177        TCGA-F1-6874        TCGA-F1-6875        TCGA-FP-7735 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-FP-7829        TCGA-FP-7916        TCGA-FP-7998        TCGA-FP-8099 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-FP-8209        TCGA-FP-8210        TCGA-FP-8631        TCGA-HJ-7597 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-IN-7806        TCGA-IN-7808        TCGA-IP-7968 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
D39V3, binary
[1] "tbl2"
                   cls
clus                [,1] [,2]
  2P LOSS CNV          2    1
  2P LOSS WILD-TYPE   70  107
        clus
vv       2P LOSS CNV 2P LOSS WILD-TYPE
  FEMALE           2                70
  MALE             1               107
                   vv
clus                STOMACH  ADENOCARCINOMA  DIFFUSE TYPE
  2P LOSS CNV                                           0
  2P LOSS WILD-TYPE                                    10
                   vv
clus                STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  2P LOSS CNV                                                            1
  2P LOSS WILD-TYPE                                                     15
                   vv
clus                STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  2P LOSS CNV                                                                       0
  2P LOSS WILD-TYPE                                                                 8
                   vv
clus                STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE
  2P LOSS CNV                                                              0
  2P LOSS WILD-TYPE                                                        3
                   vv
clus                STOMACH ADENOCARCINOMA  SIGNET RING TYPE
  2P LOSS CNV                                              0
  2P LOSS WILD-TYPE                                        1
                   vv
clus                STOMACH ADENOCARCINOMA - DIFFUSE TYPE
  2P LOSS CNV                                           0
  2P LOSS WILD-TYPE                                    16
                   vv
clus                STOMACH ADENOCARCINOMA - NOT OTHERWISE SPECIFIED (NOS)
  2P LOSS CNV                                                            0
  2P LOSS WILD-TYPE                                                     73
                   vv
clus                STOMACH INTESTINAL ADENOCARCINOMA - MUCINOUS TYPE
  2P LOSS CNV                                                       1
  2P LOSS WILD-TYPE                                                 6
                   vv
clus                STOMACH INTESTINAL ADENOCARCINOMA - PAPILLARY TYPE
  2P LOSS CNV                                                        0
  2P LOSS WILD-TYPE                                                  3
                   vv
clus                STOMACH INTESTINAL ADENOCARCINOMA - TUBULAR TYPE
  2P LOSS CNV                                                      0
  2P LOSS WILD-TYPE                                               10
                   vv
clus                STOMACH INTESTINAL ADENOCARCINOMA - TYPE NOT OTHERWISE SPECIFIED (NOS)
  2P LOSS CNV                                                                            0
  2P LOSS WILD-TYPE                                                                     28
D39V4, multiclass
[1] "Remove cluster labels:" "2P LOSS CNV"           
clus
      2P LOSS CNV 2P LOSS WILD-TYPE 
                2               173 
       TCGA-B7-5816        TCGA-B7-5818        TCGA-BR-4183        TCGA-BR-4184 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-BR-4187        TCGA-BR-4188        TCGA-BR-4191        TCGA-BR-4201 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-BR-4253        TCGA-BR-4255        TCGA-BR-4256        TCGA-BR-4257 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-BR-4267        TCGA-BR-4279        TCGA-BR-4280        TCGA-BR-4292 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-BR-4294        TCGA-BR-4357        TCGA-BR-4361        TCGA-BR-4362 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-BR-4363        TCGA-BR-4366        TCGA-BR-4367        TCGA-BR-4368 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-BR-4369        TCGA-BR-4370        TCGA-BR-4371        TCGA-BR-6452 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-BR-6453        TCGA-BR-6454        TCGA-BR-6455        TCGA-BR-6456 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-BR-6457        TCGA-BR-6458        TCGA-BR-6563        TCGA-BR-6564 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-BR-6565        TCGA-BR-6566        TCGA-BR-6705        TCGA-BR-6706 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-BR-6707        TCGA-BR-6709        TCGA-BR-6710        TCGA-BR-6801 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-BR-6802        TCGA-BR-6803        TCGA-BR-6852        TCGA-BR-7196 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-BR-7197        TCGA-BR-7703        TCGA-BR-7704        TCGA-BR-7707 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-BR-7715        TCGA-BR-7716        TCGA-BR-7717        TCGA-BR-7722 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-BR-7723        TCGA-BR-7851        TCGA-BR-7901        TCGA-BR-7957 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-BR-7958        TCGA-BR-7959        TCGA-BR-8059        TCGA-BR-8077 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-BR-8078        TCGA-BR-8080        TCGA-BR-8081        TCGA-BR-8284 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-BR-8285        TCGA-BR-8286        TCGA-BR-8289        TCGA-BR-8291 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-BR-8295        TCGA-BR-8296        TCGA-BR-8297        TCGA-BR-8592 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-BR-A4IU        TCGA-BR-A4IV        TCGA-BR-A4IY        TCGA-BR-A4IZ 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-BR-A4J1        TCGA-BR-A4J2        TCGA-BR-A4J4        TCGA-BR-A4J5 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-BR-A4J6        TCGA-BR-A4J8        TCGA-BR-A4J9        TCGA-BR-A4PF 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-BR-A4QI        TCGA-BR-A4QL        TCGA-CD-5798        TCGA-CD-5799 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-CD-5800        TCGA-CD-5801        TCGA-CD-5802        TCGA-CD-5803 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-CD-5804        TCGA-CG-4300        TCGA-CG-4301        TCGA-CG-4304 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-CG-4305        TCGA-CG-4306        TCGA-CG-4436        TCGA-CG-4437 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-CG-4438        TCGA-CG-4440        TCGA-CG-4441        TCGA-CG-4442 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-CG-4443        TCGA-CG-4449        TCGA-CG-4455        TCGA-CG-4460 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-CG-4466        TCGA-CG-4469        TCGA-CG-4474        TCGA-CG-4476 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-CG-4477        TCGA-CG-5716        TCGA-CG-5717        TCGA-CG-5718 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-CG-5719        TCGA-CG-5720        TCGA-CG-5721        TCGA-CG-5722 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-CG-5723        TCGA-CG-5724        TCGA-CG-5725        TCGA-CG-5726 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-CG-5727        TCGA-CG-5728        TCGA-CG-5730        TCGA-CG-5732 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-CG-5733        TCGA-CG-5734        TCGA-D7-5577        TCGA-D7-5578 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-D7-5579        TCGA-D7-6518        TCGA-D7-6519        TCGA-D7-6520 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-D7-6521        TCGA-D7-6522        TCGA-D7-6524        TCGA-D7-6525 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-D7-6526        TCGA-D7-6527        TCGA-D7-6528        TCGA-D7-6815 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-D7-6817        TCGA-D7-6818        TCGA-D7-6820        TCGA-D7-6822 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-EQ-5647        TCGA-EQ-8122        TCGA-F1-6177        TCGA-F1-6874 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-F1-6875        TCGA-FP-7735        TCGA-FP-7829        TCGA-FP-7916 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-FP-7998        TCGA-FP-8099        TCGA-FP-8209        TCGA-FP-8210 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-FP-8631        TCGA-HF-7131        TCGA-HF-7132        TCGA-HF-7134 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-HF-7136        TCGA-HJ-7597        TCGA-IN-7806        TCGA-IN-7808 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-IP-7968 
"2P LOSS WILD-TYPE" 
                   vv
clus                T1 T2 T3 T4
  2P LOSS CNV        0  1  1  0
  2P LOSS WILD-TYPE  6 51 55 18
D39V5, multiclass
[1] "Remove cluster labels:" "2P LOSS CNV"           
clus
      2P LOSS CNV 2P LOSS WILD-TYPE 
                2               130 
       TCGA-B7-5816        TCGA-B7-5818        TCGA-BR-4183        TCGA-BR-4184 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-BR-4201        TCGA-BR-4253        TCGA-BR-4255        TCGA-BR-4267 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-BR-4279        TCGA-BR-4280        TCGA-BR-4292        TCGA-BR-4294 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-BR-4357        TCGA-BR-4361        TCGA-BR-4363        TCGA-BR-4368 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-BR-4371        TCGA-BR-6452        TCGA-BR-6453        TCGA-BR-6454 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-BR-6455        TCGA-BR-6456        TCGA-BR-6457        TCGA-BR-6458 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-BR-6563        TCGA-BR-6564        TCGA-BR-6565        TCGA-BR-6566 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-BR-6705        TCGA-BR-6706        TCGA-BR-6707        TCGA-BR-6709 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-BR-6710        TCGA-BR-6801        TCGA-BR-6802        TCGA-BR-6803 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-BR-6852        TCGA-BR-7196        TCGA-BR-7197        TCGA-BR-7703 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-BR-7704        TCGA-BR-7707        TCGA-BR-7715        TCGA-BR-7716 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-BR-7717        TCGA-BR-7722        TCGA-BR-7723        TCGA-BR-7851 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-BR-7901        TCGA-BR-7957        TCGA-CD-5798        TCGA-CD-5799 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-CD-5800        TCGA-CD-5801        TCGA-CD-5802        TCGA-CD-5803 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-CD-5804        TCGA-CG-4300        TCGA-CG-4301        TCGA-CG-4304 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-CG-4305        TCGA-CG-4306        TCGA-CG-4436        TCGA-CG-4437 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-CG-4438        TCGA-CG-4440        TCGA-CG-4441        TCGA-CG-4442 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-CG-4443        TCGA-CG-4444        TCGA-CG-4449        TCGA-CG-4455 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-CG-4460        TCGA-CG-4462        TCGA-CG-4465        TCGA-CG-4466 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-CG-4469        TCGA-CG-4472        TCGA-CG-4474        TCGA-CG-4476 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-CG-4477        TCGA-CG-5716        TCGA-CG-5717        TCGA-CG-5718 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-CG-5719        TCGA-CG-5720        TCGA-CG-5721        TCGA-CG-5722 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-CG-5723        TCGA-CG-5724        TCGA-CG-5725        TCGA-CG-5726 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-CG-5727        TCGA-CG-5728        TCGA-CG-5730        TCGA-CG-5732 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-CG-5733        TCGA-CG-5734        TCGA-D7-5577        TCGA-D7-5578 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-D7-5579        TCGA-D7-6518        TCGA-D7-6519        TCGA-D7-6520 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-D7-6521        TCGA-D7-6522        TCGA-D7-6524        TCGA-D7-6525 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-D7-6526        TCGA-D7-6527        TCGA-D7-6528        TCGA-D7-6815 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-D7-6817        TCGA-D7-6818        TCGA-D7-6820        TCGA-D7-6822 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-EQ-5647        TCGA-F1-6177        TCGA-F1-6874        TCGA-F1-6875 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-FP-7735        TCGA-FP-7829        TCGA-FP-7998        TCGA-HF-7131 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-HF-7132        TCGA-HF-7134        TCGA-HF-7136        TCGA-IN-7806 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-IN-7808        TCGA-IP-7968 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
                   vv
clus                N0 N1 N2 N3
  2P LOSS CNV        0  1  0  1
  2P LOSS WILD-TYPE 44 48 23 14
D39V6, multiclass
[1] "Remove cluster labels:" "2P LOSS CNV"           
clus
      2P LOSS CNV 2P LOSS WILD-TYPE 
                2               129 
       TCGA-B7-5816        TCGA-B7-5818        TCGA-BR-4183        TCGA-BR-4184 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-BR-4188        TCGA-BR-4191        TCGA-BR-4253        TCGA-BR-4255 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-BR-4256        TCGA-BR-4267        TCGA-BR-4279        TCGA-BR-4280 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-BR-4361        TCGA-BR-4362        TCGA-BR-4367        TCGA-BR-4368 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-BR-6452        TCGA-BR-6453        TCGA-BR-6454        TCGA-BR-6455 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-BR-6456        TCGA-BR-6457        TCGA-BR-6458        TCGA-BR-6563 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-BR-6564        TCGA-BR-6565        TCGA-BR-6566        TCGA-BR-6705 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-BR-6706        TCGA-BR-6707        TCGA-BR-6709        TCGA-BR-6710 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-BR-6801        TCGA-BR-6802        TCGA-BR-6803        TCGA-BR-6852 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-BR-7196        TCGA-BR-7197        TCGA-BR-7703        TCGA-BR-7704 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-BR-7707        TCGA-BR-7715        TCGA-BR-7716        TCGA-BR-7717 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-BR-7722        TCGA-BR-7723        TCGA-BR-7851        TCGA-BR-7901 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-BR-7957        TCGA-CD-5798        TCGA-CD-5799        TCGA-CD-5800 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-CD-5801        TCGA-CD-5802        TCGA-CD-5803        TCGA-CD-5804 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-CG-4300        TCGA-CG-4301        TCGA-CG-4304        TCGA-CG-4305 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-CG-4306        TCGA-CG-4436        TCGA-CG-4437        TCGA-CG-4438 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-CG-4440        TCGA-CG-4441        TCGA-CG-4442        TCGA-CG-4443 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-CG-4444        TCGA-CG-4449        TCGA-CG-4455        TCGA-CG-4460 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-CG-4462        TCGA-CG-4465        TCGA-CG-4466        TCGA-CG-4469 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-CG-4472        TCGA-CG-4474        TCGA-CG-4476        TCGA-CG-4477 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-CG-5716        TCGA-CG-5717        TCGA-CG-5718        TCGA-CG-5719 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-CG-5720        TCGA-CG-5721        TCGA-CG-5722        TCGA-CG-5723 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-CG-5724        TCGA-CG-5725        TCGA-CG-5726        TCGA-CG-5727 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-CG-5728        TCGA-CG-5730        TCGA-CG-5732        TCGA-CG-5733 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-CG-5734        TCGA-D7-5577        TCGA-D7-5578        TCGA-D7-5579 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-D7-6518        TCGA-D7-6519        TCGA-D7-6520        TCGA-D7-6521 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-D7-6522        TCGA-D7-6524        TCGA-D7-6525        TCGA-D7-6526 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-D7-6527        TCGA-D7-6528        TCGA-D7-6815        TCGA-D7-6817 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-D7-6818        TCGA-D7-6820        TCGA-D7-6822        TCGA-EQ-5647 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-F1-6177        TCGA-F1-6874        TCGA-F1-6875        TCGA-FP-7735 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-FP-7829        TCGA-FP-7998        TCGA-HF-7131        TCGA-HF-7132 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-HF-7134        TCGA-HF-7136        TCGA-IN-7806        TCGA-IN-7808 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-IP-7968 
"2P LOSS WILD-TYPE" 
                   vv
clus                 M0  M1  MX
  2P LOSS CNV         2   0   0
  2P LOSS WILD-TYPE 116  16   8
D39V7, multiclass
[1] "Remove cluster labels:" "2P LOSS CNV"           
clus
      2P LOSS CNV 2P LOSS WILD-TYPE 
                2               140 
       TCGA-B7-5816        TCGA-B7-5818        TCGA-BR-4183        TCGA-BR-4184 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-BR-4187        TCGA-BR-4188        TCGA-BR-4191        TCGA-BR-4201 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-BR-4253        TCGA-BR-4255        TCGA-BR-4256        TCGA-BR-4257 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-BR-4267        TCGA-BR-4279        TCGA-BR-4280        TCGA-BR-4292 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-BR-4294        TCGA-BR-4357        TCGA-BR-4361        TCGA-BR-4362 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-BR-4363        TCGA-BR-4366        TCGA-BR-4367        TCGA-BR-4368 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-BR-4369        TCGA-BR-4370        TCGA-BR-4371        TCGA-BR-6452 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-BR-6453        TCGA-BR-6454        TCGA-BR-6455        TCGA-BR-6456 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-BR-6457        TCGA-BR-6458        TCGA-BR-6563        TCGA-BR-6564 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-BR-6565        TCGA-BR-6566        TCGA-BR-6705        TCGA-BR-6706 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-BR-6707        TCGA-BR-6709        TCGA-BR-6710        TCGA-BR-6801 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-BR-6802        TCGA-BR-6803        TCGA-BR-6852        TCGA-BR-7196 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-BR-7197        TCGA-BR-7703        TCGA-BR-7704        TCGA-BR-7707 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-BR-7715        TCGA-BR-7716        TCGA-BR-7717        TCGA-BR-7722 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-BR-7723        TCGA-BR-7851        TCGA-BR-7901        TCGA-BR-7957 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-CD-5798        TCGA-CD-5799        TCGA-CD-5800        TCGA-CD-5801 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-CD-5802        TCGA-CD-5803        TCGA-CD-5804        TCGA-CG-4300 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-CG-4301        TCGA-CG-4304        TCGA-CG-4305        TCGA-CG-4306 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-CG-4436        TCGA-CG-4437        TCGA-CG-4438        TCGA-CG-4440 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-CG-4441        TCGA-CG-4442        TCGA-CG-4443        TCGA-CG-4444 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-CG-4449        TCGA-CG-4455        TCGA-CG-4460        TCGA-CG-4462 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-CG-4465        TCGA-CG-4466        TCGA-CG-4469        TCGA-CG-4472 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-CG-4474        TCGA-CG-4476        TCGA-CG-4477        TCGA-CG-5716 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-CG-5717        TCGA-CG-5718        TCGA-CG-5719        TCGA-CG-5720 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-CG-5721        TCGA-CG-5722        TCGA-CG-5723        TCGA-CG-5724 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-CG-5725        TCGA-CG-5726        TCGA-CG-5727        TCGA-CG-5728 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-CG-5730        TCGA-CG-5732        TCGA-CG-5733        TCGA-CG-5734 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-D7-5577        TCGA-D7-5578        TCGA-D7-5579        TCGA-D7-6518 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-D7-6519        TCGA-D7-6520        TCGA-D7-6521        TCGA-D7-6522 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-D7-6524        TCGA-D7-6525        TCGA-D7-6526        TCGA-D7-6527 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-D7-6528        TCGA-D7-6815        TCGA-D7-6817        TCGA-D7-6818 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-D7-6820        TCGA-D7-6822        TCGA-EQ-5647        TCGA-F1-6177 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-F1-6874        TCGA-F1-6875        TCGA-FP-7735        TCGA-FP-7829 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-FP-7998        TCGA-HF-7131        TCGA-HF-7132        TCGA-HF-7134 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-HF-7136        TCGA-IN-7806        TCGA-IN-7808        TCGA-IP-7968 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
                   vv
clus                 I II III IV
  2P LOSS CNV        0  1   0  1
  2P LOSS WILD-TYPE 24 36  39 25
D39V8, multiclass
[1] "Remove cluster labels:" "2P LOSS CNV"           
clus
      2P LOSS CNV 2P LOSS WILD-TYPE 
                2               124 
       TCGA-B7-5816        TCGA-B7-5818        TCGA-BR-4183        TCGA-BR-4184 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-BR-4253        TCGA-BR-4255        TCGA-BR-4267        TCGA-BR-4279 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-BR-4280        TCGA-BR-4361        TCGA-BR-4368        TCGA-BR-6452 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-BR-6453        TCGA-BR-6454        TCGA-BR-6455        TCGA-BR-6456 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-BR-6457        TCGA-BR-6458        TCGA-BR-6563        TCGA-BR-6564 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-BR-6565        TCGA-BR-6566        TCGA-BR-6705        TCGA-BR-6706 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-BR-6707        TCGA-BR-6709        TCGA-BR-6710        TCGA-BR-6801 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-BR-6802        TCGA-BR-6803        TCGA-BR-6852        TCGA-BR-7196 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-BR-7197        TCGA-BR-7703        TCGA-BR-7704        TCGA-BR-7707 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-BR-7715        TCGA-BR-7716        TCGA-BR-7717        TCGA-BR-7722 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-BR-7723        TCGA-BR-7851        TCGA-BR-7901        TCGA-BR-7957 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-CD-5798        TCGA-CD-5799        TCGA-CD-5800        TCGA-CD-5801 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-CD-5802        TCGA-CD-5803        TCGA-CD-5804        TCGA-CG-4300 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-CG-4301        TCGA-CG-4304        TCGA-CG-4305        TCGA-CG-4306 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-CG-4436        TCGA-CG-4437        TCGA-CG-4438        TCGA-CG-4440 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-CG-4441        TCGA-CG-4442        TCGA-CG-4443        TCGA-CG-4444 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-CG-4449        TCGA-CG-4455        TCGA-CG-4460        TCGA-CG-4462 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-CG-4465        TCGA-CG-4466        TCGA-CG-4469        TCGA-CG-4472 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-CG-4474        TCGA-CG-4476        TCGA-CG-4477        TCGA-CG-5716 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-CG-5717        TCGA-CG-5718        TCGA-CG-5719        TCGA-CG-5720 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-CG-5721        TCGA-CG-5722        TCGA-CG-5723        TCGA-CG-5724 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-CG-5725        TCGA-CG-5726        TCGA-CG-5727        TCGA-CG-5728 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-CG-5730        TCGA-CG-5732        TCGA-CG-5733        TCGA-CG-5734 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-D7-5577        TCGA-D7-5578        TCGA-D7-5579        TCGA-D7-6518 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-D7-6519        TCGA-D7-6520        TCGA-D7-6521        TCGA-D7-6522 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-D7-6524        TCGA-D7-6525        TCGA-D7-6526        TCGA-D7-6527 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-D7-6528        TCGA-D7-6815        TCGA-D7-6817        TCGA-D7-6818 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-D7-6820        TCGA-D7-6822        TCGA-EQ-5647        TCGA-F1-6177 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-F1-6874        TCGA-F1-6875        TCGA-FP-7735        TCGA-FP-7829 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-FP-7998        TCGA-HF-7131        TCGA-HF-7132        TCGA-HF-7134 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-HF-7136        TCGA-IN-7806        TCGA-IN-7808        TCGA-IP-7968 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
D39V9, binary
[1] "tbl2"
                   cls
clus                [,1] [,2]
  2P LOSS CNV          1    2
  2P LOSS WILD-TYPE    4  173
     clus
vv    2P LOSS CNV 2P LOSS WILD-TYPE
  NO            1                 4
  YES           2               173
                   vv
clus                 R0  R1  R2  RX
  2P LOSS CNV         2   1   0   0
  2P LOSS WILD-TYPE 123   6  12  25
D39V10, multiclass
    clus
vv   2P LOSS CNV 2P LOSS WILD-TYPE
  R0           2               123
  R1           1                 6
  R2           0                12
  RX           0                25
D39V11, continuous
[1] "Remove cluster labels:" "2P LOSS CNV"           
clus
      2P LOSS CNV 2P LOSS WILD-TYPE 
                2               134 
       TCGA-B7-5816        TCGA-BR-4183        TCGA-BR-4184        TCGA-BR-4188 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-BR-4191        TCGA-BR-4253        TCGA-BR-4255        TCGA-BR-4256 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-BR-4267        TCGA-BR-4279        TCGA-BR-4280        TCGA-BR-4361 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-BR-4362        TCGA-BR-4367        TCGA-BR-4368        TCGA-BR-6452 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-BR-6453        TCGA-BR-6454        TCGA-BR-6455        TCGA-BR-6456 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-BR-6457        TCGA-BR-6458        TCGA-BR-6563        TCGA-BR-6564 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-BR-6565        TCGA-BR-6566        TCGA-BR-6705        TCGA-BR-6706 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-BR-6707        TCGA-BR-6709        TCGA-BR-6710        TCGA-BR-6801 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-BR-6802        TCGA-BR-6803        TCGA-BR-6852        TCGA-BR-7196 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-BR-7197        TCGA-BR-7703        TCGA-BR-7704        TCGA-BR-7707 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-BR-7715        TCGA-BR-7716        TCGA-BR-7717        TCGA-BR-7722 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-BR-7723        TCGA-BR-7851        TCGA-BR-7901        TCGA-BR-7957 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-BR-7958        TCGA-BR-7959        TCGA-BR-8059        TCGA-BR-8077 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-BR-8078        TCGA-BR-8080        TCGA-BR-8081        TCGA-BR-8284 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-BR-8285        TCGA-BR-8286        TCGA-BR-8289        TCGA-BR-8291 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-BR-8295        TCGA-BR-8296        TCGA-BR-8297        TCGA-BR-8592 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-BR-A4IU        TCGA-BR-A4IV        TCGA-BR-A4IY        TCGA-BR-A4IZ 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-BR-A4J1        TCGA-BR-A4J2        TCGA-BR-A4J4        TCGA-BR-A4J5 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-BR-A4J6        TCGA-BR-A4J8        TCGA-BR-A4J9        TCGA-BR-A4PF 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-BR-A4QI        TCGA-BR-A4QL        TCGA-CD-5804        TCGA-CG-5717 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-CG-5718        TCGA-CG-5719        TCGA-CG-5720        TCGA-CG-5721 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-CG-5722        TCGA-CG-5723        TCGA-CG-5724        TCGA-CG-5725 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-CG-5726        TCGA-CG-5727        TCGA-CG-5728        TCGA-CG-5730 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-CG-5732        TCGA-CG-5733        TCGA-CG-5734        TCGA-D7-5577 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-D7-5578        TCGA-D7-5579        TCGA-D7-6518        TCGA-D7-6519 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-D7-6520        TCGA-D7-6521        TCGA-D7-6522        TCGA-D7-6524 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-D7-6525        TCGA-D7-6526        TCGA-D7-6527        TCGA-D7-6528 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-D7-6815        TCGA-D7-6817        TCGA-D7-6818        TCGA-D7-6820 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-D7-6822        TCGA-EQ-5647        TCGA-EQ-8122        TCGA-F1-6177 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-F1-6874        TCGA-F1-6875        TCGA-FP-7735        TCGA-FP-7829 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-FP-7916        TCGA-FP-7998        TCGA-FP-8099        TCGA-FP-8209 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-FP-8210        TCGA-FP-8631        TCGA-HF-7131        TCGA-HF-7132 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-HF-7134        TCGA-HF-7136        TCGA-HJ-7597        TCGA-IN-7806 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-IN-7808        TCGA-IP-7968 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 

Clustering(40) Variable = 3p loss
D40V1, survival
                   sevent
clus2                 0   1
  3P LOSS CNV        13   2
  3P LOSS WILD-TYPE 111  17
      3P LOSS CNV 3P LOSS WILD-TYPE 
               15               128 
      3P LOSS CNV 3P LOSS WILD-TYPE 
                2                17 
$`3P LOSS CNV`
TCGA-BR-6458 TCGA-BR-7715 TCGA-BR-A4J1 TCGA-BR-A4J4 TCGA-BR-A4PF TCGA-BR-A4QI 
        1.35         1.05         0.72         0.53         0.72         0.49 
TCGA-CG-4438 TCGA-CG-4466 TCGA-CG-5725 TCGA-CG-5730 TCGA-D7-6525 TCGA-D7-6528 
       54.05        18.94        15.02         4.01         5.95         1.68 
TCGA-FP-7829 TCGA-FP-8631 TCGA-IN-7806 
        0.20         0.56         6.87 

$`3P LOSS WILD-TYPE`
TCGA-B7-5816 TCGA-B7-5818 TCGA-BR-6452 TCGA-BR-6455 TCGA-BR-6457 TCGA-BR-6563 
        5.62         0.10         0.95         1.41         1.35         0.85 
TCGA-BR-6564 TCGA-BR-6565 TCGA-BR-6566 TCGA-BR-6705 TCGA-BR-6706 TCGA-BR-6707 
        0.82         0.62         0.62         1.71         2.17         0.99 
TCGA-BR-6709 TCGA-BR-6710 TCGA-BR-6801 TCGA-BR-6802 TCGA-BR-6803 TCGA-BR-6852 
        1.22         0.66         1.12         0.76         0.66         0.26 
TCGA-BR-7196 TCGA-BR-7197 TCGA-BR-7703 TCGA-BR-7704 TCGA-BR-7707 TCGA-BR-7716 
        1.22         1.48         0.46         1.25         0.13         0.82 
TCGA-BR-7717 TCGA-BR-7722 TCGA-BR-7723 TCGA-BR-7851 TCGA-BR-7901 TCGA-BR-7957 
        0.69         0.16         4.54         0.99         0.95         0.69 
TCGA-BR-7958 TCGA-BR-7959 TCGA-BR-8059 TCGA-BR-8060 TCGA-BR-8077 TCGA-BR-8078 
        0.16         1.08         0.82         1.32         0.69         0.95 
TCGA-BR-8080 TCGA-BR-8081 TCGA-BR-8284 TCGA-BR-8285 TCGA-BR-8286 TCGA-BR-8289 
        0.49         0.46         0.72         0.26         0.43         0.26 
TCGA-BR-8291 TCGA-BR-8295 TCGA-BR-8296 TCGA-BR-8297 TCGA-BR-8592 TCGA-BR-A4IU 
        1.18         1.55         1.48         0.76         0.20         0.59 
TCGA-BR-A4IV TCGA-BR-A4IY TCGA-BR-A4IZ TCGA-BR-A4J2 TCGA-BR-A4J5 TCGA-BR-A4J6 
        0.92         0.39         0.79         0.79         0.43         0.13 
TCGA-BR-A4J8 TCGA-BR-A4J9 TCGA-BR-A4QL TCGA-CD-5798 TCGA-CD-5799 TCGA-CD-5800 
        0.23         0.10         2.24         0.82         0.69         0.36 
TCGA-CD-5801 TCGA-CD-5802 TCGA-CD-5803 TCGA-CG-4300 TCGA-CG-4301 TCGA-CG-4304 
        0.49         0.30         0.07        20.02         3.02        27.02 
TCGA-CG-4305 TCGA-CG-4306 TCGA-CG-4436 TCGA-CG-4437 TCGA-CG-4440 TCGA-CG-4441 
       15.95         1.02        52.96         8.05         4.01        14.01 
TCGA-CG-4443 TCGA-CG-4444 TCGA-CG-4449 TCGA-CG-4455 TCGA-CG-4460 TCGA-CG-4462 
       29.98        47.05        19.07        12.03        21.99         1.02 
TCGA-CG-4465 TCGA-CG-4469 TCGA-CG-4472 TCGA-CG-4474 TCGA-CG-4477 TCGA-CG-5716 
        8.98         7.07        12.00         1.02         1.02         1.02 
TCGA-CG-5717 TCGA-CG-5718 TCGA-CG-5719 TCGA-CG-5720 TCGA-CG-5721 TCGA-CG-5722 
        6.94         1.02         1.02         0.99         5.98         0.95 
TCGA-CG-5723 TCGA-CG-5724 TCGA-CG-5726 TCGA-CG-5727 TCGA-CG-5728 TCGA-CG-5732 
       70.06        12.03        28.96        31.04        65.10        55.04 
TCGA-CG-5733 TCGA-CG-5734 TCGA-D7-5577 TCGA-D7-5578 TCGA-D7-5579 TCGA-D7-6518 
       21.07         7.99         8.65         3.58         4.54         9.80 
TCGA-D7-6519 TCGA-D7-6520 TCGA-D7-6521 TCGA-D7-6522 TCGA-D7-6524 TCGA-D7-6526 
       15.65         9.63         8.19         6.90         0.69         6.61 
TCGA-D7-6527 TCGA-D7-6815 TCGA-D7-6817 TCGA-D7-6818 TCGA-D7-6820 TCGA-D7-6822 
        4.14         3.65         4.70         4.04         2.93         4.27 
TCGA-EQ-5647 TCGA-EQ-8122 TCGA-F1-6177 TCGA-F1-6874 TCGA-F1-6875 TCGA-FP-7735 
        0.62         7.79         6.54         2.01        72.23         0.39 
TCGA-FP-7916 TCGA-FP-7998 TCGA-FP-8099 TCGA-FP-8209 TCGA-FP-8210 TCGA-HJ-7597 
        3.02         3.58         1.02        59.05         5.03        26.43 
TCGA-IN-7808 TCGA-IP-7968 
        3.55         2.53 

      3P LOSS CNV 3P LOSS WILD-TYPE 
             0.20              0.07 
      3P LOSS CNV 3P LOSS WILD-TYPE 
            54.05             72.23 
      3P LOSS CNV 3P LOSS WILD-TYPE 
            1.350             1.235 
[1] "0.2 - 54.0 (1.4)" "0.1 - 72.2 (1.2)"
       TCGA-B7-5816        TCGA-B7-5818        TCGA-BR-6452        TCGA-BR-6455 
"3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" 
       TCGA-BR-6457        TCGA-BR-6458        TCGA-BR-6563        TCGA-BR-6564 
"3P LOSS WILD-TYPE"       "3P LOSS CNV" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" 
       TCGA-BR-6565        TCGA-BR-6566        TCGA-BR-6705        TCGA-BR-6706 
"3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" 
       TCGA-BR-6707        TCGA-BR-6709        TCGA-BR-6710        TCGA-BR-6801 
"3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" 
       TCGA-BR-6802        TCGA-BR-6803        TCGA-BR-6852        TCGA-BR-7196 
"3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" 
       TCGA-BR-7197        TCGA-BR-7703        TCGA-BR-7704        TCGA-BR-7707 
"3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" 
       TCGA-BR-7715        TCGA-BR-7716        TCGA-BR-7717        TCGA-BR-7722 
      "3P LOSS CNV" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" 
       TCGA-BR-7723        TCGA-BR-7851        TCGA-BR-7901        TCGA-BR-7957 
"3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" 
       TCGA-BR-7958        TCGA-BR-7959        TCGA-BR-8059        TCGA-BR-8060 
"3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" 
       TCGA-BR-8077        TCGA-BR-8078        TCGA-BR-8080        TCGA-BR-8081 
"3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" 
       TCGA-BR-8284        TCGA-BR-8285        TCGA-BR-8286        TCGA-BR-8289 
"3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" 
       TCGA-BR-8291        TCGA-BR-8295        TCGA-BR-8296        TCGA-BR-8297 
"3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" 
       TCGA-BR-8592        TCGA-BR-A4IU        TCGA-BR-A4IV        TCGA-BR-A4IY 
"3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" 
       TCGA-BR-A4IZ        TCGA-BR-A4J1        TCGA-BR-A4J2        TCGA-BR-A4J4 
"3P LOSS WILD-TYPE"       "3P LOSS CNV" "3P LOSS WILD-TYPE"       "3P LOSS CNV" 
       TCGA-BR-A4J5        TCGA-BR-A4J6        TCGA-BR-A4J8        TCGA-BR-A4J9 
"3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" 
       TCGA-BR-A4PF        TCGA-BR-A4QI        TCGA-BR-A4QL        TCGA-CD-5798 
      "3P LOSS CNV"       "3P LOSS CNV" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" 
       TCGA-CD-5799        TCGA-CD-5800        TCGA-CD-5801        TCGA-CD-5802 
"3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" 
       TCGA-CD-5803        TCGA-CG-4300        TCGA-CG-4301        TCGA-CG-4304 
"3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" 
       TCGA-CG-4305        TCGA-CG-4306        TCGA-CG-4436        TCGA-CG-4437 
"3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" 
       TCGA-CG-4438        TCGA-CG-4440        TCGA-CG-4441        TCGA-CG-4443 
      "3P LOSS CNV" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" 
       TCGA-CG-4444        TCGA-CG-4449        TCGA-CG-4455        TCGA-CG-4460 
"3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" 
       TCGA-CG-4462        TCGA-CG-4465        TCGA-CG-4466        TCGA-CG-4469 
"3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE"       "3P LOSS CNV" "3P LOSS WILD-TYPE" 
       TCGA-CG-4472        TCGA-CG-4474        TCGA-CG-4477        TCGA-CG-5716 
"3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" 
       TCGA-CG-5717        TCGA-CG-5718        TCGA-CG-5719        TCGA-CG-5720 
"3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" 
       TCGA-CG-5721        TCGA-CG-5722        TCGA-CG-5723        TCGA-CG-5724 
"3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" 
       TCGA-CG-5725        TCGA-CG-5726        TCGA-CG-5727        TCGA-CG-5728 
      "3P LOSS CNV" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" 
       TCGA-CG-5730        TCGA-CG-5732        TCGA-CG-5733        TCGA-CG-5734 
      "3P LOSS CNV" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" 
       TCGA-D7-5577        TCGA-D7-5578        TCGA-D7-5579        TCGA-D7-6518 
"3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" 
       TCGA-D7-6519        TCGA-D7-6520        TCGA-D7-6521        TCGA-D7-6522 
"3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" 
       TCGA-D7-6524        TCGA-D7-6525        TCGA-D7-6526        TCGA-D7-6527 
"3P LOSS WILD-TYPE"       "3P LOSS CNV" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" 
       TCGA-D7-6528        TCGA-D7-6815        TCGA-D7-6817        TCGA-D7-6818 
      "3P LOSS CNV" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" 
       TCGA-D7-6820        TCGA-D7-6822        TCGA-EQ-5647        TCGA-EQ-8122 
"3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" 
       TCGA-F1-6177        TCGA-F1-6874        TCGA-F1-6875        TCGA-FP-7735 
"3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" 
       TCGA-FP-7829        TCGA-FP-7916        TCGA-FP-7998        TCGA-FP-8099 
      "3P LOSS CNV" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" 
       TCGA-FP-8209        TCGA-FP-8210        TCGA-FP-8631        TCGA-HJ-7597 
"3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE"       "3P LOSS CNV" "3P LOSS WILD-TYPE" 
       TCGA-IN-7806        TCGA-IN-7808        TCGA-IP-7968 
      "3P LOSS CNV" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" 
       TCGA-B7-5816        TCGA-B7-5818        TCGA-BR-6452        TCGA-BR-6455 
"3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" 
       TCGA-BR-6457        TCGA-BR-6458        TCGA-BR-6563        TCGA-BR-6564 
"3P LOSS WILD-TYPE"       "3P LOSS CNV" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" 
       TCGA-BR-6565        TCGA-BR-6566        TCGA-BR-6705        TCGA-BR-6706 
"3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" 
       TCGA-BR-6707        TCGA-BR-6709        TCGA-BR-6710        TCGA-BR-6801 
"3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" 
       TCGA-BR-6802        TCGA-BR-6803        TCGA-BR-6852        TCGA-BR-7196 
"3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" 
       TCGA-BR-7197        TCGA-BR-7703        TCGA-BR-7704        TCGA-BR-7707 
"3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" 
       TCGA-BR-7715        TCGA-BR-7716        TCGA-BR-7717        TCGA-BR-7722 
      "3P LOSS CNV" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" 
       TCGA-BR-7723        TCGA-BR-7851        TCGA-BR-7901        TCGA-BR-7957 
"3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" 
       TCGA-BR-7958        TCGA-BR-7959        TCGA-BR-8059        TCGA-BR-8060 
"3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" 
       TCGA-BR-8077        TCGA-BR-8078        TCGA-BR-8080        TCGA-BR-8081 
"3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" 
       TCGA-BR-8284        TCGA-BR-8285        TCGA-BR-8286        TCGA-BR-8289 
"3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" 
       TCGA-BR-8291        TCGA-BR-8295        TCGA-BR-8296        TCGA-BR-8297 
"3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" 
       TCGA-BR-8592        TCGA-BR-A4IU        TCGA-BR-A4IV        TCGA-BR-A4IY 
"3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" 
       TCGA-BR-A4IZ        TCGA-BR-A4J1        TCGA-BR-A4J2        TCGA-BR-A4J4 
"3P LOSS WILD-TYPE"       "3P LOSS CNV" "3P LOSS WILD-TYPE"       "3P LOSS CNV" 
       TCGA-BR-A4J5        TCGA-BR-A4J6        TCGA-BR-A4J8        TCGA-BR-A4J9 
"3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" 
       TCGA-BR-A4PF        TCGA-BR-A4QI        TCGA-BR-A4QL        TCGA-CD-5798 
      "3P LOSS CNV"       "3P LOSS CNV" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" 
       TCGA-CD-5799        TCGA-CD-5800        TCGA-CD-5801        TCGA-CD-5802 
"3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" 
       TCGA-CD-5803        TCGA-CG-4300        TCGA-CG-4301        TCGA-CG-4304 
"3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" 
       TCGA-CG-4305        TCGA-CG-4306        TCGA-CG-4436        TCGA-CG-4437 
"3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" 
       TCGA-CG-4438        TCGA-CG-4440        TCGA-CG-4441        TCGA-CG-4443 
      "3P LOSS CNV" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" 
       TCGA-CG-4444        TCGA-CG-4449        TCGA-CG-4455        TCGA-CG-4460 
"3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" 
       TCGA-CG-4462        TCGA-CG-4465        TCGA-CG-4466        TCGA-CG-4469 
"3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE"       "3P LOSS CNV" "3P LOSS WILD-TYPE" 
       TCGA-CG-4472        TCGA-CG-4474        TCGA-CG-4477        TCGA-CG-5716 
"3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" 
       TCGA-CG-5717        TCGA-CG-5718        TCGA-CG-5719        TCGA-CG-5720 
"3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" 
       TCGA-CG-5721        TCGA-CG-5722        TCGA-CG-5723        TCGA-CG-5724 
"3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" 
       TCGA-CG-5725        TCGA-CG-5726        TCGA-CG-5727        TCGA-CG-5728 
      "3P LOSS CNV" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" 
       TCGA-CG-5730        TCGA-CG-5732        TCGA-CG-5733        TCGA-CG-5734 
      "3P LOSS CNV" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" 
       TCGA-D7-5577        TCGA-D7-5578        TCGA-D7-5579        TCGA-D7-6518 
"3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" 
       TCGA-D7-6519        TCGA-D7-6520        TCGA-D7-6521        TCGA-D7-6522 
"3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" 
       TCGA-D7-6524        TCGA-D7-6525        TCGA-D7-6526        TCGA-D7-6527 
"3P LOSS WILD-TYPE"       "3P LOSS CNV" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" 
       TCGA-D7-6528        TCGA-D7-6815        TCGA-D7-6817        TCGA-D7-6818 
      "3P LOSS CNV" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" 
       TCGA-D7-6820        TCGA-D7-6822        TCGA-EQ-5647        TCGA-EQ-8122 
"3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" 
       TCGA-F1-6177        TCGA-F1-6874        TCGA-F1-6875        TCGA-FP-7735 
"3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" 
       TCGA-FP-7829        TCGA-FP-7916        TCGA-FP-7998        TCGA-FP-8099 
      "3P LOSS CNV" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" 
       TCGA-FP-8209        TCGA-FP-8210        TCGA-FP-8631        TCGA-HJ-7597 
"3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE"       "3P LOSS CNV" "3P LOSS WILD-TYPE" 
       TCGA-IN-7806        TCGA-IN-7808        TCGA-IP-7968 
      "3P LOSS CNV" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" 
       TCGA-B7-5816        TCGA-B7-5818        TCGA-BR-6452        TCGA-BR-6455 
"3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" 
       TCGA-BR-6457        TCGA-BR-6458        TCGA-BR-6563        TCGA-BR-6564 
"3P LOSS WILD-TYPE"       "3P LOSS CNV" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" 
       TCGA-BR-6565        TCGA-BR-6566        TCGA-BR-6705        TCGA-BR-6706 
"3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" 
       TCGA-BR-6707        TCGA-BR-6709        TCGA-BR-6710        TCGA-BR-6801 
"3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" 
       TCGA-BR-6802        TCGA-BR-6803        TCGA-BR-6852        TCGA-BR-7196 
"3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" 
       TCGA-BR-7197        TCGA-BR-7703        TCGA-BR-7704        TCGA-BR-7707 
"3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" 
       TCGA-BR-7715        TCGA-BR-7716        TCGA-BR-7717        TCGA-BR-7722 
      "3P LOSS CNV" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" 
       TCGA-BR-7723        TCGA-BR-7851        TCGA-BR-7901        TCGA-BR-7957 
"3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" 
       TCGA-BR-7958        TCGA-BR-7959        TCGA-BR-8059        TCGA-BR-8060 
"3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" 
       TCGA-BR-8077        TCGA-BR-8078        TCGA-BR-8080        TCGA-BR-8081 
"3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" 
       TCGA-BR-8284        TCGA-BR-8285        TCGA-BR-8286        TCGA-BR-8289 
"3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" 
       TCGA-BR-8291        TCGA-BR-8295        TCGA-BR-8296        TCGA-BR-8297 
"3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" 
       TCGA-BR-8592        TCGA-BR-A4IU        TCGA-BR-A4IV        TCGA-BR-A4IY 
"3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" 
       TCGA-BR-A4IZ        TCGA-BR-A4J1        TCGA-BR-A4J2        TCGA-BR-A4J4 
"3P LOSS WILD-TYPE"       "3P LOSS CNV" "3P LOSS WILD-TYPE"       "3P LOSS CNV" 
       TCGA-BR-A4J5        TCGA-BR-A4J6        TCGA-BR-A4J8        TCGA-BR-A4J9 
"3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" 
       TCGA-BR-A4PF        TCGA-BR-A4QI        TCGA-BR-A4QL        TCGA-CD-5798 
      "3P LOSS CNV"       "3P LOSS CNV" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" 
       TCGA-CD-5799        TCGA-CD-5800        TCGA-CD-5801        TCGA-CD-5802 
"3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" 
       TCGA-CD-5803        TCGA-CG-4300        TCGA-CG-4301        TCGA-CG-4304 
"3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" 
       TCGA-CG-4305        TCGA-CG-4306        TCGA-CG-4436        TCGA-CG-4437 
"3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" 
       TCGA-CG-4438        TCGA-CG-4440        TCGA-CG-4441        TCGA-CG-4443 
      "3P LOSS CNV" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" 
       TCGA-CG-4444        TCGA-CG-4449        TCGA-CG-4455        TCGA-CG-4460 
"3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" 
       TCGA-CG-4462        TCGA-CG-4465        TCGA-CG-4466        TCGA-CG-4469 
"3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE"       "3P LOSS CNV" "3P LOSS WILD-TYPE" 
       TCGA-CG-4472        TCGA-CG-4474        TCGA-CG-4477        TCGA-CG-5716 
"3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" 
       TCGA-CG-5717        TCGA-CG-5718        TCGA-CG-5719        TCGA-CG-5720 
"3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" 
       TCGA-CG-5721        TCGA-CG-5722        TCGA-CG-5723        TCGA-CG-5724 
"3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" 
       TCGA-CG-5725        TCGA-CG-5726        TCGA-CG-5727        TCGA-CG-5728 
      "3P LOSS CNV" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" 
       TCGA-CG-5730        TCGA-CG-5732        TCGA-CG-5733        TCGA-CG-5734 
      "3P LOSS CNV" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" 
       TCGA-D7-5577        TCGA-D7-5578        TCGA-D7-5579        TCGA-D7-6518 
"3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" 
       TCGA-D7-6519        TCGA-D7-6520        TCGA-D7-6521        TCGA-D7-6522 
"3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" 
       TCGA-D7-6524        TCGA-D7-6525        TCGA-D7-6526        TCGA-D7-6527 
"3P LOSS WILD-TYPE"       "3P LOSS CNV" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" 
       TCGA-D7-6528        TCGA-D7-6815        TCGA-D7-6817        TCGA-D7-6818 
      "3P LOSS CNV" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" 
       TCGA-D7-6820        TCGA-D7-6822        TCGA-EQ-5647        TCGA-EQ-8122 
"3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" 
       TCGA-F1-6177        TCGA-F1-6874        TCGA-F1-6875        TCGA-FP-7735 
"3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" 
       TCGA-FP-7829        TCGA-FP-7916        TCGA-FP-7998        TCGA-FP-8099 
      "3P LOSS CNV" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" 
       TCGA-FP-8209        TCGA-FP-8210        TCGA-FP-8631        TCGA-HJ-7597 
"3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE"       "3P LOSS CNV" "3P LOSS WILD-TYPE" 
       TCGA-IN-7806        TCGA-IN-7808        TCGA-IP-7968 
      "3P LOSS CNV" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" 
[1] "hr=" "1.2"
D40V2, continuous
D40V3, binary
[1] "tbl2"
                   cls
clus                [,1] [,2]
  3P LOSS CNV          5   10
  3P LOSS WILD-TYPE   67   98
        clus
vv       3P LOSS CNV 3P LOSS WILD-TYPE
  FEMALE           5                67
  MALE            10                98
                   vv
clus                STOMACH  ADENOCARCINOMA  DIFFUSE TYPE
  3P LOSS CNV                                           0
  3P LOSS WILD-TYPE                                    10
                   vv
clus                STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  3P LOSS CNV                                                            4
  3P LOSS WILD-TYPE                                                     12
                   vv
clus                STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  3P LOSS CNV                                                                       1
  3P LOSS WILD-TYPE                                                                 7
                   vv
clus                STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE
  3P LOSS CNV                                                              0
  3P LOSS WILD-TYPE                                                        3
                   vv
clus                STOMACH ADENOCARCINOMA  SIGNET RING TYPE
  3P LOSS CNV                                              0
  3P LOSS WILD-TYPE                                        1
                   vv
clus                STOMACH ADENOCARCINOMA - DIFFUSE TYPE
  3P LOSS CNV                                           2
  3P LOSS WILD-TYPE                                    14
                   vv
clus                STOMACH ADENOCARCINOMA - NOT OTHERWISE SPECIFIED (NOS)
  3P LOSS CNV                                                            3
  3P LOSS WILD-TYPE                                                     70
                   vv
clus                STOMACH INTESTINAL ADENOCARCINOMA - MUCINOUS TYPE
  3P LOSS CNV                                                       1
  3P LOSS WILD-TYPE                                                 6
                   vv
clus                STOMACH INTESTINAL ADENOCARCINOMA - PAPILLARY TYPE
  3P LOSS CNV                                                        0
  3P LOSS WILD-TYPE                                                  3
                   vv
clus                STOMACH INTESTINAL ADENOCARCINOMA - TUBULAR TYPE
  3P LOSS CNV                                                      1
  3P LOSS WILD-TYPE                                                9
                   vv
clus                STOMACH INTESTINAL ADENOCARCINOMA - TYPE NOT OTHERWISE SPECIFIED (NOS)
  3P LOSS CNV                                                                            3
  3P LOSS WILD-TYPE                                                                     25
D40V4, multiclass
                   vv
clus                T1 T2 T3 T4
  3P LOSS CNV        0  5  4  1
  3P LOSS WILD-TYPE  6 47 52 17
D40V5, multiclass
    clus
vv   3P LOSS CNV 3P LOSS WILD-TYPE
  T1           0                 6
  T2           5                47
  T3           4                52
  T4           1                17
                   vv
clus                N0 N1 N2 N3
  3P LOSS CNV        4  4  2  0
  3P LOSS WILD-TYPE 40 45 21 15
D40V6, multiclass
    clus
vv   3P LOSS CNV 3P LOSS WILD-TYPE
  N0           4                40
  N1           4                45
  N2           2                21
  N3           0                15
                   vv
clus                 M0  M1  MX
  3P LOSS CNV         9   1   0
  3P LOSS WILD-TYPE 109  15   8
D40V7, multiclass
    clus
vv   3P LOSS CNV 3P LOSS WILD-TYPE
  M0           9               109
  M1           1                15
  MX           0                 8
                   vv
clus                 I II III IV
  3P LOSS CNV        3  2   3  2
  3P LOSS WILD-TYPE 21 35  36 24
D40V8, multiclass
     clus
vv    3P LOSS CNV 3P LOSS WILD-TYPE
  I             3                21
  II            2                35
  III           3                36
  IV            2                24
D40V9, binary
[1] "tbl2"
                   cls
clus                [,1] [,2]
  3P LOSS CNV          0   15
  3P LOSS WILD-TYPE    5  160
     clus
vv    3P LOSS CNV 3P LOSS WILD-TYPE
  NO            0                 5
  YES          15               160
                   vv
clus                 R0  R1  R2  RX
  3P LOSS CNV        14   0   1   0
  3P LOSS WILD-TYPE 111   7  11  25
D40V10, multiclass
    clus
vv   3P LOSS CNV 3P LOSS WILD-TYPE
  R0          14               111
  R1           0                 7
  R2           1                11
  RX           0                25
D40V11, continuous

Clustering(41) Variable = 3q loss
D41V1, survival
                   sevent
clus2                 0   1
  3Q LOSS CNV         7   2
  3Q LOSS WILD-TYPE 117  17
      3Q LOSS CNV 3Q LOSS WILD-TYPE 
                9               134 
      3Q LOSS CNV 3Q LOSS WILD-TYPE 
                2                17 
$`3Q LOSS CNV`
TCGA-BR-7715 TCGA-BR-A4J1 TCGA-BR-A4PF TCGA-BR-A4QI TCGA-CG-4438 TCGA-CG-4466 
        1.05         0.72         0.72         0.49        54.05        18.94 
TCGA-CG-5725 TCGA-FP-7829 TCGA-IN-7806 
       15.02         0.20         6.87 

$`3Q LOSS WILD-TYPE`
TCGA-B7-5816 TCGA-B7-5818 TCGA-BR-6452 TCGA-BR-6455 TCGA-BR-6457 TCGA-BR-6458 
        5.62         0.10         0.95         1.41         1.35         1.35 
TCGA-BR-6563 TCGA-BR-6564 TCGA-BR-6565 TCGA-BR-6566 TCGA-BR-6705 TCGA-BR-6706 
        0.85         0.82         0.62         0.62         1.71         2.17 
TCGA-BR-6707 TCGA-BR-6709 TCGA-BR-6710 TCGA-BR-6801 TCGA-BR-6802 TCGA-BR-6803 
        0.99         1.22         0.66         1.12         0.76         0.66 
TCGA-BR-6852 TCGA-BR-7196 TCGA-BR-7197 TCGA-BR-7703 TCGA-BR-7704 TCGA-BR-7707 
        0.26         1.22         1.48         0.46         1.25         0.13 
TCGA-BR-7716 TCGA-BR-7717 TCGA-BR-7722 TCGA-BR-7723 TCGA-BR-7851 TCGA-BR-7901 
        0.82         0.69         0.16         4.54         0.99         0.95 
TCGA-BR-7957 TCGA-BR-7958 TCGA-BR-7959 TCGA-BR-8059 TCGA-BR-8060 TCGA-BR-8077 
        0.69         0.16         1.08         0.82         1.32         0.69 
TCGA-BR-8078 TCGA-BR-8080 TCGA-BR-8081 TCGA-BR-8284 TCGA-BR-8285 TCGA-BR-8286 
        0.95         0.49         0.46         0.72         0.26         0.43 
TCGA-BR-8289 TCGA-BR-8291 TCGA-BR-8295 TCGA-BR-8296 TCGA-BR-8297 TCGA-BR-8592 
        0.26         1.18         1.55         1.48         0.76         0.20 
TCGA-BR-A4IU TCGA-BR-A4IV TCGA-BR-A4IY TCGA-BR-A4IZ TCGA-BR-A4J2 TCGA-BR-A4J4 
        0.59         0.92         0.39         0.79         0.79         0.53 
TCGA-BR-A4J5 TCGA-BR-A4J6 TCGA-BR-A4J8 TCGA-BR-A4J9 TCGA-BR-A4QL TCGA-CD-5798 
        0.43         0.13         0.23         0.10         2.24         0.82 
TCGA-CD-5799 TCGA-CD-5800 TCGA-CD-5801 TCGA-CD-5802 TCGA-CD-5803 TCGA-CG-4300 
        0.69         0.36         0.49         0.30         0.07        20.02 
TCGA-CG-4301 TCGA-CG-4304 TCGA-CG-4305 TCGA-CG-4306 TCGA-CG-4436 TCGA-CG-4437 
        3.02        27.02        15.95         1.02        52.96         8.05 
TCGA-CG-4440 TCGA-CG-4441 TCGA-CG-4443 TCGA-CG-4444 TCGA-CG-4449 TCGA-CG-4455 
        4.01        14.01        29.98        47.05        19.07        12.03 
TCGA-CG-4460 TCGA-CG-4462 TCGA-CG-4465 TCGA-CG-4469 TCGA-CG-4472 TCGA-CG-4474 
       21.99         1.02         8.98         7.07        12.00         1.02 
TCGA-CG-4477 TCGA-CG-5716 TCGA-CG-5717 TCGA-CG-5718 TCGA-CG-5719 TCGA-CG-5720 
        1.02         1.02         6.94         1.02         1.02         0.99 
TCGA-CG-5721 TCGA-CG-5722 TCGA-CG-5723 TCGA-CG-5724 TCGA-CG-5726 TCGA-CG-5727 
        5.98         0.95        70.06        12.03        28.96        31.04 
TCGA-CG-5728 TCGA-CG-5730 TCGA-CG-5732 TCGA-CG-5733 TCGA-CG-5734 TCGA-D7-5577 
       65.10         4.01        55.04        21.07         7.99         8.65 
TCGA-D7-5578 TCGA-D7-5579 TCGA-D7-6518 TCGA-D7-6519 TCGA-D7-6520 TCGA-D7-6521 
        3.58         4.54         9.80        15.65         9.63         8.19 
TCGA-D7-6522 TCGA-D7-6524 TCGA-D7-6525 TCGA-D7-6526 TCGA-D7-6527 TCGA-D7-6528 
        6.90         0.69         5.95         6.61         4.14         1.68 
TCGA-D7-6815 TCGA-D7-6817 TCGA-D7-6818 TCGA-D7-6820 TCGA-D7-6822 TCGA-EQ-5647 
        3.65         4.70         4.04         2.93         4.27         0.62 
TCGA-EQ-8122 TCGA-F1-6177 TCGA-F1-6874 TCGA-F1-6875 TCGA-FP-7735 TCGA-FP-7916 
        7.79         6.54         2.01        72.23         0.39         3.02 
TCGA-FP-7998 TCGA-FP-8099 TCGA-FP-8209 TCGA-FP-8210 TCGA-FP-8631 TCGA-HJ-7597 
        3.58         1.02        59.05         5.03         0.56        26.43 
TCGA-IN-7808 TCGA-IP-7968 
        3.55         2.53 

      3Q LOSS CNV 3Q LOSS WILD-TYPE 
             0.20              0.07 
      3Q LOSS CNV 3Q LOSS WILD-TYPE 
            54.05             72.23 
      3Q LOSS CNV 3Q LOSS WILD-TYPE 
            1.050             1.285 
[1] "0.2 - 54.0 (1.1)" "0.1 - 72.2 (1.3)"
       TCGA-B7-5816        TCGA-B7-5818        TCGA-BR-6452        TCGA-BR-6455 
"3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" 
       TCGA-BR-6457        TCGA-BR-6458        TCGA-BR-6563        TCGA-BR-6564 
"3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" 
       TCGA-BR-6565        TCGA-BR-6566        TCGA-BR-6705        TCGA-BR-6706 
"3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" 
       TCGA-BR-6707        TCGA-BR-6709        TCGA-BR-6710        TCGA-BR-6801 
"3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" 
       TCGA-BR-6802        TCGA-BR-6803        TCGA-BR-6852        TCGA-BR-7196 
"3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" 
       TCGA-BR-7197        TCGA-BR-7703        TCGA-BR-7704        TCGA-BR-7707 
"3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" 
       TCGA-BR-7715        TCGA-BR-7716        TCGA-BR-7717        TCGA-BR-7722 
      "3Q LOSS CNV" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" 
       TCGA-BR-7723        TCGA-BR-7851        TCGA-BR-7901        TCGA-BR-7957 
"3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" 
       TCGA-BR-7958        TCGA-BR-7959        TCGA-BR-8059        TCGA-BR-8060 
"3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" 
       TCGA-BR-8077        TCGA-BR-8078        TCGA-BR-8080        TCGA-BR-8081 
"3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" 
       TCGA-BR-8284        TCGA-BR-8285        TCGA-BR-8286        TCGA-BR-8289 
"3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" 
       TCGA-BR-8291        TCGA-BR-8295        TCGA-BR-8296        TCGA-BR-8297 
"3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" 
       TCGA-BR-8592        TCGA-BR-A4IU        TCGA-BR-A4IV        TCGA-BR-A4IY 
"3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" 
       TCGA-BR-A4IZ        TCGA-BR-A4J1        TCGA-BR-A4J2        TCGA-BR-A4J4 
"3Q LOSS WILD-TYPE"       "3Q LOSS CNV" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" 
       TCGA-BR-A4J5        TCGA-BR-A4J6        TCGA-BR-A4J8        TCGA-BR-A4J9 
"3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" 
       TCGA-BR-A4PF        TCGA-BR-A4QI        TCGA-BR-A4QL        TCGA-CD-5798 
      "3Q LOSS CNV"       "3Q LOSS CNV" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" 
       TCGA-CD-5799        TCGA-CD-5800        TCGA-CD-5801        TCGA-CD-5802 
"3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" 
       TCGA-CD-5803        TCGA-CG-4300        TCGA-CG-4301        TCGA-CG-4304 
"3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" 
       TCGA-CG-4305        TCGA-CG-4306        TCGA-CG-4436        TCGA-CG-4437 
"3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" 
       TCGA-CG-4438        TCGA-CG-4440        TCGA-CG-4441        TCGA-CG-4443 
      "3Q LOSS CNV" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" 
       TCGA-CG-4444        TCGA-CG-4449        TCGA-CG-4455        TCGA-CG-4460 
"3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" 
       TCGA-CG-4462        TCGA-CG-4465        TCGA-CG-4466        TCGA-CG-4469 
"3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE"       "3Q LOSS CNV" "3Q LOSS WILD-TYPE" 
       TCGA-CG-4472        TCGA-CG-4474        TCGA-CG-4477        TCGA-CG-5716 
"3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" 
       TCGA-CG-5717        TCGA-CG-5718        TCGA-CG-5719        TCGA-CG-5720 
"3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" 
       TCGA-CG-5721        TCGA-CG-5722        TCGA-CG-5723        TCGA-CG-5724 
"3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" 
       TCGA-CG-5725        TCGA-CG-5726        TCGA-CG-5727        TCGA-CG-5728 
      "3Q LOSS CNV" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" 
       TCGA-CG-5730        TCGA-CG-5732        TCGA-CG-5733        TCGA-CG-5734 
"3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" 
       TCGA-D7-5577        TCGA-D7-5578        TCGA-D7-5579        TCGA-D7-6518 
"3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" 
       TCGA-D7-6519        TCGA-D7-6520        TCGA-D7-6521        TCGA-D7-6522 
"3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" 
       TCGA-D7-6524        TCGA-D7-6525        TCGA-D7-6526        TCGA-D7-6527 
"3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" 
       TCGA-D7-6528        TCGA-D7-6815        TCGA-D7-6817        TCGA-D7-6818 
"3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" 
       TCGA-D7-6820        TCGA-D7-6822        TCGA-EQ-5647        TCGA-EQ-8122 
"3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" 
       TCGA-F1-6177        TCGA-F1-6874        TCGA-F1-6875        TCGA-FP-7735 
"3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" 
       TCGA-FP-7829        TCGA-FP-7916        TCGA-FP-7998        TCGA-FP-8099 
      "3Q LOSS CNV" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" 
       TCGA-FP-8209        TCGA-FP-8210        TCGA-FP-8631        TCGA-HJ-7597 
"3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" 
       TCGA-IN-7806        TCGA-IN-7808        TCGA-IP-7968 
      "3Q LOSS CNV" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" 
       TCGA-B7-5816        TCGA-B7-5818        TCGA-BR-6452        TCGA-BR-6455 
"3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" 
       TCGA-BR-6457        TCGA-BR-6458        TCGA-BR-6563        TCGA-BR-6564 
"3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" 
       TCGA-BR-6565        TCGA-BR-6566        TCGA-BR-6705        TCGA-BR-6706 
"3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" 
       TCGA-BR-6707        TCGA-BR-6709        TCGA-BR-6710        TCGA-BR-6801 
"3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" 
       TCGA-BR-6802        TCGA-BR-6803        TCGA-BR-6852        TCGA-BR-7196 
"3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" 
       TCGA-BR-7197        TCGA-BR-7703        TCGA-BR-7704        TCGA-BR-7707 
"3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" 
       TCGA-BR-7715        TCGA-BR-7716        TCGA-BR-7717        TCGA-BR-7722 
      "3Q LOSS CNV" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" 
       TCGA-BR-7723        TCGA-BR-7851        TCGA-BR-7901        TCGA-BR-7957 
"3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" 
       TCGA-BR-7958        TCGA-BR-7959        TCGA-BR-8059        TCGA-BR-8060 
"3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" 
       TCGA-BR-8077        TCGA-BR-8078        TCGA-BR-8080        TCGA-BR-8081 
"3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" 
       TCGA-BR-8284        TCGA-BR-8285        TCGA-BR-8286        TCGA-BR-8289 
"3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" 
       TCGA-BR-8291        TCGA-BR-8295        TCGA-BR-8296        TCGA-BR-8297 
"3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" 
       TCGA-BR-8592        TCGA-BR-A4IU        TCGA-BR-A4IV        TCGA-BR-A4IY 
"3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" 
       TCGA-BR-A4IZ        TCGA-BR-A4J1        TCGA-BR-A4J2        TCGA-BR-A4J4 
"3Q LOSS WILD-TYPE"       "3Q LOSS CNV" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" 
       TCGA-BR-A4J5        TCGA-BR-A4J6        TCGA-BR-A4J8        TCGA-BR-A4J9 
"3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" 
       TCGA-BR-A4PF        TCGA-BR-A4QI        TCGA-BR-A4QL        TCGA-CD-5798 
      "3Q LOSS CNV"       "3Q LOSS CNV" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" 
       TCGA-CD-5799        TCGA-CD-5800        TCGA-CD-5801        TCGA-CD-5802 
"3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" 
       TCGA-CD-5803        TCGA-CG-4300        TCGA-CG-4301        TCGA-CG-4304 
"3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" 
       TCGA-CG-4305        TCGA-CG-4306        TCGA-CG-4436        TCGA-CG-4437 
"3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" 
       TCGA-CG-4438        TCGA-CG-4440        TCGA-CG-4441        TCGA-CG-4443 
      "3Q LOSS CNV" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" 
       TCGA-CG-4444        TCGA-CG-4449        TCGA-CG-4455        TCGA-CG-4460 
"3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" 
       TCGA-CG-4462        TCGA-CG-4465        TCGA-CG-4466        TCGA-CG-4469 
"3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE"       "3Q LOSS CNV" "3Q LOSS WILD-TYPE" 
       TCGA-CG-4472        TCGA-CG-4474        TCGA-CG-4477        TCGA-CG-5716 
"3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" 
       TCGA-CG-5717        TCGA-CG-5718        TCGA-CG-5719        TCGA-CG-5720 
"3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" 
       TCGA-CG-5721        TCGA-CG-5722        TCGA-CG-5723        TCGA-CG-5724 
"3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" 
       TCGA-CG-5725        TCGA-CG-5726        TCGA-CG-5727        TCGA-CG-5728 
      "3Q LOSS CNV" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" 
       TCGA-CG-5730        TCGA-CG-5732        TCGA-CG-5733        TCGA-CG-5734 
"3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" 
       TCGA-D7-5577        TCGA-D7-5578        TCGA-D7-5579        TCGA-D7-6518 
"3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" 
       TCGA-D7-6519        TCGA-D7-6520        TCGA-D7-6521        TCGA-D7-6522 
"3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" 
       TCGA-D7-6524        TCGA-D7-6525        TCGA-D7-6526        TCGA-D7-6527 
"3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" 
       TCGA-D7-6528        TCGA-D7-6815        TCGA-D7-6817        TCGA-D7-6818 
"3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" 
       TCGA-D7-6820        TCGA-D7-6822        TCGA-EQ-5647        TCGA-EQ-8122 
"3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" 
       TCGA-F1-6177        TCGA-F1-6874        TCGA-F1-6875        TCGA-FP-7735 
"3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" 
       TCGA-FP-7829        TCGA-FP-7916        TCGA-FP-7998        TCGA-FP-8099 
      "3Q LOSS CNV" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" 
       TCGA-FP-8209        TCGA-FP-8210        TCGA-FP-8631        TCGA-HJ-7597 
"3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" 
       TCGA-IN-7806        TCGA-IN-7808        TCGA-IP-7968 
      "3Q LOSS CNV" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" 
       TCGA-B7-5816        TCGA-B7-5818        TCGA-BR-6452        TCGA-BR-6455 
"3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" 
       TCGA-BR-6457        TCGA-BR-6458        TCGA-BR-6563        TCGA-BR-6564 
"3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" 
       TCGA-BR-6565        TCGA-BR-6566        TCGA-BR-6705        TCGA-BR-6706 
"3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" 
       TCGA-BR-6707        TCGA-BR-6709        TCGA-BR-6710        TCGA-BR-6801 
"3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" 
       TCGA-BR-6802        TCGA-BR-6803        TCGA-BR-6852        TCGA-BR-7196 
"3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" 
       TCGA-BR-7197        TCGA-BR-7703        TCGA-BR-7704        TCGA-BR-7707 
"3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" 
       TCGA-BR-7715        TCGA-BR-7716        TCGA-BR-7717        TCGA-BR-7722 
      "3Q LOSS CNV" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" 
       TCGA-BR-7723        TCGA-BR-7851        TCGA-BR-7901        TCGA-BR-7957 
"3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" 
       TCGA-BR-7958        TCGA-BR-7959        TCGA-BR-8059        TCGA-BR-8060 
"3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" 
       TCGA-BR-8077        TCGA-BR-8078        TCGA-BR-8080        TCGA-BR-8081 
"3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" 
       TCGA-BR-8284        TCGA-BR-8285        TCGA-BR-8286        TCGA-BR-8289 
"3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" 
       TCGA-BR-8291        TCGA-BR-8295        TCGA-BR-8296        TCGA-BR-8297 
"3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" 
       TCGA-BR-8592        TCGA-BR-A4IU        TCGA-BR-A4IV        TCGA-BR-A4IY 
"3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" 
       TCGA-BR-A4IZ        TCGA-BR-A4J1        TCGA-BR-A4J2        TCGA-BR-A4J4 
"3Q LOSS WILD-TYPE"       "3Q LOSS CNV" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" 
       TCGA-BR-A4J5        TCGA-BR-A4J6        TCGA-BR-A4J8        TCGA-BR-A4J9 
"3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" 
       TCGA-BR-A4PF        TCGA-BR-A4QI        TCGA-BR-A4QL        TCGA-CD-5798 
      "3Q LOSS CNV"       "3Q LOSS CNV" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" 
       TCGA-CD-5799        TCGA-CD-5800        TCGA-CD-5801        TCGA-CD-5802 
"3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" 
       TCGA-CD-5803        TCGA-CG-4300        TCGA-CG-4301        TCGA-CG-4304 
"3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" 
       TCGA-CG-4305        TCGA-CG-4306        TCGA-CG-4436        TCGA-CG-4437 
"3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" 
       TCGA-CG-4438        TCGA-CG-4440        TCGA-CG-4441        TCGA-CG-4443 
      "3Q LOSS CNV" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" 
       TCGA-CG-4444        TCGA-CG-4449        TCGA-CG-4455        TCGA-CG-4460 
"3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" 
       TCGA-CG-4462        TCGA-CG-4465        TCGA-CG-4466        TCGA-CG-4469 
"3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE"       "3Q LOSS CNV" "3Q LOSS WILD-TYPE" 
       TCGA-CG-4472        TCGA-CG-4474        TCGA-CG-4477        TCGA-CG-5716 
"3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" 
       TCGA-CG-5717        TCGA-CG-5718        TCGA-CG-5719        TCGA-CG-5720 
"3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" 
       TCGA-CG-5721        TCGA-CG-5722        TCGA-CG-5723        TCGA-CG-5724 
"3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" 
       TCGA-CG-5725        TCGA-CG-5726        TCGA-CG-5727        TCGA-CG-5728 
      "3Q LOSS CNV" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" 
       TCGA-CG-5730        TCGA-CG-5732        TCGA-CG-5733        TCGA-CG-5734 
"3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" 
       TCGA-D7-5577        TCGA-D7-5578        TCGA-D7-5579        TCGA-D7-6518 
"3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" 
       TCGA-D7-6519        TCGA-D7-6520        TCGA-D7-6521        TCGA-D7-6522 
"3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" 
       TCGA-D7-6524        TCGA-D7-6525        TCGA-D7-6526        TCGA-D7-6527 
"3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" 
       TCGA-D7-6528        TCGA-D7-6815        TCGA-D7-6817        TCGA-D7-6818 
"3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" 
       TCGA-D7-6820        TCGA-D7-6822        TCGA-EQ-5647        TCGA-EQ-8122 
"3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" 
       TCGA-F1-6177        TCGA-F1-6874        TCGA-F1-6875        TCGA-FP-7735 
"3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" 
       TCGA-FP-7829        TCGA-FP-7916        TCGA-FP-7998        TCGA-FP-8099 
      "3Q LOSS CNV" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" 
       TCGA-FP-8209        TCGA-FP-8210        TCGA-FP-8631        TCGA-HJ-7597 
"3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" 
       TCGA-IN-7806        TCGA-IN-7808        TCGA-IP-7968 
      "3Q LOSS CNV" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" 
[1] "hr=" "1.4"
D41V2, continuous
D41V3, binary
[1] "tbl2"
                   cls
clus                [,1] [,2]
  3Q LOSS CNV          2    7
  3Q LOSS WILD-TYPE   70  101
        clus
vv       3Q LOSS CNV 3Q LOSS WILD-TYPE
  FEMALE           2                70
  MALE             7               101
                   vv
clus                STOMACH  ADENOCARCINOMA  DIFFUSE TYPE
  3Q LOSS CNV                                           0
  3Q LOSS WILD-TYPE                                    10
                   vv
clus                STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  3Q LOSS CNV                                                            3
  3Q LOSS WILD-TYPE                                                     13
                   vv
clus                STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  3Q LOSS CNV                                                                       0
  3Q LOSS WILD-TYPE                                                                 8
                   vv
clus                STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE
  3Q LOSS CNV                                                              0
  3Q LOSS WILD-TYPE                                                        3
                   vv
clus                STOMACH ADENOCARCINOMA  SIGNET RING TYPE
  3Q LOSS CNV                                              0
  3Q LOSS WILD-TYPE                                        1
                   vv
clus                STOMACH ADENOCARCINOMA - DIFFUSE TYPE
  3Q LOSS CNV                                           1
  3Q LOSS WILD-TYPE                                    15
                   vv
clus                STOMACH ADENOCARCINOMA - NOT OTHERWISE SPECIFIED (NOS)
  3Q LOSS CNV                                                            2
  3Q LOSS WILD-TYPE                                                     71
                   vv
clus                STOMACH INTESTINAL ADENOCARCINOMA - MUCINOUS TYPE
  3Q LOSS CNV                                                       1
  3Q LOSS WILD-TYPE                                                 6
                   vv
clus                STOMACH INTESTINAL ADENOCARCINOMA - PAPILLARY TYPE
  3Q LOSS CNV                                                        0
  3Q LOSS WILD-TYPE                                                  3
                   vv
clus                STOMACH INTESTINAL ADENOCARCINOMA - TUBULAR TYPE
  3Q LOSS CNV                                                      0
  3Q LOSS WILD-TYPE                                               10
                   vv
clus                STOMACH INTESTINAL ADENOCARCINOMA - TYPE NOT OTHERWISE SPECIFIED (NOS)
  3Q LOSS CNV                                                                            2
  3Q LOSS WILD-TYPE                                                                     26
D41V4, multiclass
                   vv
clus                T1 T2 T3 T4
  3Q LOSS CNV        0  2  3  1
  3Q LOSS WILD-TYPE  6 50 53 17
D41V5, multiclass
    clus
vv   3Q LOSS CNV 3Q LOSS WILD-TYPE
  T1           0                 6
  T2           2                50
  T3           3                53
  T4           1                17
                   vv
clus                N0 N1 N2 N3
  3Q LOSS CNV        3  2  1  0
  3Q LOSS WILD-TYPE 41 47 22 15
D41V6, multiclass
    clus
vv   3Q LOSS CNV 3Q LOSS WILD-TYPE
  N0           3                41
  N1           2                47
  N2           1                22
  N3           0                15
                   vv
clus                 M0  M1  MX
  3Q LOSS CNV         6   0   0
  3Q LOSS WILD-TYPE 112  16   8
D41V7, multiclass
    clus
vv   3Q LOSS CNV 3Q LOSS WILD-TYPE
  M0           6               112
  M1           0                16
  MX           0                 8
                   vv
clus                 I II III IV
  3Q LOSS CNV        2  1   2  1
  3Q LOSS WILD-TYPE 22 36  37 25
D41V8, multiclass
     clus
vv    3Q LOSS CNV 3Q LOSS WILD-TYPE
  I             2                22
  II            1                36
  III           2                37
  IV            1                25
D41V9, binary
[1] "tbl2"
                   cls
clus                [,1] [,2]
  3Q LOSS CNV          0    9
  3Q LOSS WILD-TYPE    5  166
     clus
vv    3Q LOSS CNV 3Q LOSS WILD-TYPE
  NO            0                 5
  YES           9               166
                   vv
clus                 R0  R1  R2  RX
  3Q LOSS CNV         9   0   0   0
  3Q LOSS WILD-TYPE 116   7  12  25
D41V10, multiclass
    clus
vv   3Q LOSS CNV 3Q LOSS WILD-TYPE
  R0           9               116
  R1           0                 7
  R2           0                12
  RX           0                25
D41V11, continuous

Clustering(42) Variable = 4p loss
D42V1, survival
                   sevent
clus2                 0   1
  4P LOSS CNV        20   5
  4P LOSS WILD-TYPE 104  14
      4P LOSS CNV 4P LOSS WILD-TYPE 
               25               118 
      4P LOSS CNV 4P LOSS WILD-TYPE 
                5                14 
$`4P LOSS CNV`
TCGA-BR-7197 TCGA-BR-7723 TCGA-BR-8289 TCGA-BR-8291 TCGA-BR-8295 TCGA-BR-A4J1 
        1.48         4.54         0.26         1.18         1.55         0.72 
TCGA-BR-A4J6 TCGA-BR-A4QI TCGA-CD-5799 TCGA-CD-5802 TCGA-CG-4300 TCGA-CG-4438 
        0.13         0.49         0.69         0.30        20.02        54.05 
TCGA-CG-4440 TCGA-CG-4449 TCGA-CG-4466 TCGA-CG-4469 TCGA-CG-4477 TCGA-CG-5725 
        4.01        19.07        18.94         7.07         1.02        15.02 
TCGA-D7-6519 TCGA-D7-6527 TCGA-D7-6528 TCGA-D7-6820 TCGA-EQ-8122 TCGA-FP-8099 
       15.65         4.14         1.68         2.93         7.79         1.02 
TCGA-HJ-7597 
       26.43 

$`4P LOSS WILD-TYPE`
TCGA-B7-5816 TCGA-B7-5818 TCGA-BR-6452 TCGA-BR-6455 TCGA-BR-6457 TCGA-BR-6458 
        5.62         0.10         0.95         1.41         1.35         1.35 
TCGA-BR-6563 TCGA-BR-6564 TCGA-BR-6565 TCGA-BR-6566 TCGA-BR-6705 TCGA-BR-6706 
        0.85         0.82         0.62         0.62         1.71         2.17 
TCGA-BR-6707 TCGA-BR-6709 TCGA-BR-6710 TCGA-BR-6801 TCGA-BR-6802 TCGA-BR-6803 
        0.99         1.22         0.66         1.12         0.76         0.66 
TCGA-BR-6852 TCGA-BR-7196 TCGA-BR-7703 TCGA-BR-7704 TCGA-BR-7707 TCGA-BR-7715 
        0.26         1.22         0.46         1.25         0.13         1.05 
TCGA-BR-7716 TCGA-BR-7717 TCGA-BR-7722 TCGA-BR-7851 TCGA-BR-7901 TCGA-BR-7957 
        0.82         0.69         0.16         0.99         0.95         0.69 
TCGA-BR-7958 TCGA-BR-7959 TCGA-BR-8059 TCGA-BR-8060 TCGA-BR-8077 TCGA-BR-8078 
        0.16         1.08         0.82         1.32         0.69         0.95 
TCGA-BR-8080 TCGA-BR-8081 TCGA-BR-8284 TCGA-BR-8285 TCGA-BR-8286 TCGA-BR-8296 
        0.49         0.46         0.72         0.26         0.43         1.48 
TCGA-BR-8297 TCGA-BR-8592 TCGA-BR-A4IU TCGA-BR-A4IV TCGA-BR-A4IY TCGA-BR-A4IZ 
        0.76         0.20         0.59         0.92         0.39         0.79 
TCGA-BR-A4J2 TCGA-BR-A4J4 TCGA-BR-A4J5 TCGA-BR-A4J8 TCGA-BR-A4J9 TCGA-BR-A4PF 
        0.79         0.53         0.43         0.23         0.10         0.72 
TCGA-BR-A4QL TCGA-CD-5798 TCGA-CD-5800 TCGA-CD-5801 TCGA-CD-5803 TCGA-CG-4301 
        2.24         0.82         0.36         0.49         0.07         3.02 
TCGA-CG-4304 TCGA-CG-4305 TCGA-CG-4306 TCGA-CG-4436 TCGA-CG-4437 TCGA-CG-4441 
       27.02        15.95         1.02        52.96         8.05        14.01 
TCGA-CG-4443 TCGA-CG-4444 TCGA-CG-4455 TCGA-CG-4460 TCGA-CG-4462 TCGA-CG-4465 
       29.98        47.05        12.03        21.99         1.02         8.98 
TCGA-CG-4472 TCGA-CG-4474 TCGA-CG-5716 TCGA-CG-5717 TCGA-CG-5718 TCGA-CG-5719 
       12.00         1.02         1.02         6.94         1.02         1.02 
TCGA-CG-5720 TCGA-CG-5721 TCGA-CG-5722 TCGA-CG-5723 TCGA-CG-5724 TCGA-CG-5726 
        0.99         5.98         0.95        70.06        12.03        28.96 
TCGA-CG-5727 TCGA-CG-5728 TCGA-CG-5730 TCGA-CG-5732 TCGA-CG-5733 TCGA-CG-5734 
       31.04        65.10         4.01        55.04        21.07         7.99 
TCGA-D7-5577 TCGA-D7-5578 TCGA-D7-5579 TCGA-D7-6518 TCGA-D7-6520 TCGA-D7-6521 
        8.65         3.58         4.54         9.80         9.63         8.19 
TCGA-D7-6522 TCGA-D7-6524 TCGA-D7-6525 TCGA-D7-6526 TCGA-D7-6815 TCGA-D7-6817 
        6.90         0.69         5.95         6.61         3.65         4.70 
TCGA-D7-6818 TCGA-D7-6822 TCGA-EQ-5647 TCGA-F1-6177 TCGA-F1-6874 TCGA-F1-6875 
        4.04         4.27         0.62         6.54         2.01        72.23 
TCGA-FP-7735 TCGA-FP-7829 TCGA-FP-7916 TCGA-FP-7998 TCGA-FP-8209 TCGA-FP-8210 
        0.39         0.20         3.02         3.58        59.05         5.03 
TCGA-FP-8631 TCGA-IN-7806 TCGA-IN-7808 TCGA-IP-7968 
        0.56         6.87         3.55         2.53 

      4P LOSS CNV 4P LOSS WILD-TYPE 
             0.13              0.07 
      4P LOSS CNV 4P LOSS WILD-TYPE 
            54.05             72.23 
      4P LOSS CNV 4P LOSS WILD-TYPE 
             2.93              1.10 
[1] "0.1 - 54.0 (2.9)" "0.1 - 72.2 (1.1)"
       TCGA-B7-5816        TCGA-B7-5818        TCGA-BR-6452        TCGA-BR-6455 
"4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" 
       TCGA-BR-6457        TCGA-BR-6458        TCGA-BR-6563        TCGA-BR-6564 
"4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" 
       TCGA-BR-6565        TCGA-BR-6566        TCGA-BR-6705        TCGA-BR-6706 
"4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" 
       TCGA-BR-6707        TCGA-BR-6709        TCGA-BR-6710        TCGA-BR-6801 
"4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" 
       TCGA-BR-6802        TCGA-BR-6803        TCGA-BR-6852        TCGA-BR-7196 
"4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" 
       TCGA-BR-7197        TCGA-BR-7703        TCGA-BR-7704        TCGA-BR-7707 
      "4P LOSS CNV" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" 
       TCGA-BR-7715        TCGA-BR-7716        TCGA-BR-7717        TCGA-BR-7722 
"4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" 
       TCGA-BR-7723        TCGA-BR-7851        TCGA-BR-7901        TCGA-BR-7957 
      "4P LOSS CNV" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" 
       TCGA-BR-7958        TCGA-BR-7959        TCGA-BR-8059        TCGA-BR-8060 
"4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" 
       TCGA-BR-8077        TCGA-BR-8078        TCGA-BR-8080        TCGA-BR-8081 
"4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" 
       TCGA-BR-8284        TCGA-BR-8285        TCGA-BR-8286        TCGA-BR-8289 
"4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE"       "4P LOSS CNV" 
       TCGA-BR-8291        TCGA-BR-8295        TCGA-BR-8296        TCGA-BR-8297 
      "4P LOSS CNV"       "4P LOSS CNV" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" 
       TCGA-BR-8592        TCGA-BR-A4IU        TCGA-BR-A4IV        TCGA-BR-A4IY 
"4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" 
       TCGA-BR-A4IZ        TCGA-BR-A4J1        TCGA-BR-A4J2        TCGA-BR-A4J4 
"4P LOSS WILD-TYPE"       "4P LOSS CNV" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" 
       TCGA-BR-A4J5        TCGA-BR-A4J6        TCGA-BR-A4J8        TCGA-BR-A4J9 
"4P LOSS WILD-TYPE"       "4P LOSS CNV" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" 
       TCGA-BR-A4PF        TCGA-BR-A4QI        TCGA-BR-A4QL        TCGA-CD-5798 
"4P LOSS WILD-TYPE"       "4P LOSS CNV" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" 
       TCGA-CD-5799        TCGA-CD-5800        TCGA-CD-5801        TCGA-CD-5802 
      "4P LOSS CNV" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE"       "4P LOSS CNV" 
       TCGA-CD-5803        TCGA-CG-4300        TCGA-CG-4301        TCGA-CG-4304 
"4P LOSS WILD-TYPE"       "4P LOSS CNV" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" 
       TCGA-CG-4305        TCGA-CG-4306        TCGA-CG-4436        TCGA-CG-4437 
"4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" 
       TCGA-CG-4438        TCGA-CG-4440        TCGA-CG-4441        TCGA-CG-4443 
      "4P LOSS CNV"       "4P LOSS CNV" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" 
       TCGA-CG-4444        TCGA-CG-4449        TCGA-CG-4455        TCGA-CG-4460 
"4P LOSS WILD-TYPE"       "4P LOSS CNV" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" 
       TCGA-CG-4462        TCGA-CG-4465        TCGA-CG-4466        TCGA-CG-4469 
"4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE"       "4P LOSS CNV"       "4P LOSS CNV" 
       TCGA-CG-4472        TCGA-CG-4474        TCGA-CG-4477        TCGA-CG-5716 
"4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE"       "4P LOSS CNV" "4P LOSS WILD-TYPE" 
       TCGA-CG-5717        TCGA-CG-5718        TCGA-CG-5719        TCGA-CG-5720 
"4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" 
       TCGA-CG-5721        TCGA-CG-5722        TCGA-CG-5723        TCGA-CG-5724 
"4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" 
       TCGA-CG-5725        TCGA-CG-5726        TCGA-CG-5727        TCGA-CG-5728 
      "4P LOSS CNV" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" 
       TCGA-CG-5730        TCGA-CG-5732        TCGA-CG-5733        TCGA-CG-5734 
"4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" 
       TCGA-D7-5577        TCGA-D7-5578        TCGA-D7-5579        TCGA-D7-6518 
"4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" 
       TCGA-D7-6519        TCGA-D7-6520        TCGA-D7-6521        TCGA-D7-6522 
      "4P LOSS CNV" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" 
       TCGA-D7-6524        TCGA-D7-6525        TCGA-D7-6526        TCGA-D7-6527 
"4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE"       "4P LOSS CNV" 
       TCGA-D7-6528        TCGA-D7-6815        TCGA-D7-6817        TCGA-D7-6818 
      "4P LOSS CNV" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" 
       TCGA-D7-6820        TCGA-D7-6822        TCGA-EQ-5647        TCGA-EQ-8122 
      "4P LOSS CNV" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE"       "4P LOSS CNV" 
       TCGA-F1-6177        TCGA-F1-6874        TCGA-F1-6875        TCGA-FP-7735 
"4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" 
       TCGA-FP-7829        TCGA-FP-7916        TCGA-FP-7998        TCGA-FP-8099 
"4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE"       "4P LOSS CNV" 
       TCGA-FP-8209        TCGA-FP-8210        TCGA-FP-8631        TCGA-HJ-7597 
"4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE"       "4P LOSS CNV" 
       TCGA-IN-7806        TCGA-IN-7808        TCGA-IP-7968 
"4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" 
       TCGA-B7-5816        TCGA-B7-5818        TCGA-BR-6452        TCGA-BR-6455 
"4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" 
       TCGA-BR-6457        TCGA-BR-6458        TCGA-BR-6563        TCGA-BR-6564 
"4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" 
       TCGA-BR-6565        TCGA-BR-6566        TCGA-BR-6705        TCGA-BR-6706 
"4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" 
       TCGA-BR-6707        TCGA-BR-6709        TCGA-BR-6710        TCGA-BR-6801 
"4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" 
       TCGA-BR-6802        TCGA-BR-6803        TCGA-BR-6852        TCGA-BR-7196 
"4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" 
       TCGA-BR-7197        TCGA-BR-7703        TCGA-BR-7704        TCGA-BR-7707 
      "4P LOSS CNV" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" 
       TCGA-BR-7715        TCGA-BR-7716        TCGA-BR-7717        TCGA-BR-7722 
"4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" 
       TCGA-BR-7723        TCGA-BR-7851        TCGA-BR-7901        TCGA-BR-7957 
      "4P LOSS CNV" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" 
       TCGA-BR-7958        TCGA-BR-7959        TCGA-BR-8059        TCGA-BR-8060 
"4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" 
       TCGA-BR-8077        TCGA-BR-8078        TCGA-BR-8080        TCGA-BR-8081 
"4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" 
       TCGA-BR-8284        TCGA-BR-8285        TCGA-BR-8286        TCGA-BR-8289 
"4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE"       "4P LOSS CNV" 
       TCGA-BR-8291        TCGA-BR-8295        TCGA-BR-8296        TCGA-BR-8297 
      "4P LOSS CNV"       "4P LOSS CNV" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" 
       TCGA-BR-8592        TCGA-BR-A4IU        TCGA-BR-A4IV        TCGA-BR-A4IY 
"4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" 
       TCGA-BR-A4IZ        TCGA-BR-A4J1        TCGA-BR-A4J2        TCGA-BR-A4J4 
"4P LOSS WILD-TYPE"       "4P LOSS CNV" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" 
       TCGA-BR-A4J5        TCGA-BR-A4J6        TCGA-BR-A4J8        TCGA-BR-A4J9 
"4P LOSS WILD-TYPE"       "4P LOSS CNV" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" 
       TCGA-BR-A4PF        TCGA-BR-A4QI        TCGA-BR-A4QL        TCGA-CD-5798 
"4P LOSS WILD-TYPE"       "4P LOSS CNV" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" 
       TCGA-CD-5799        TCGA-CD-5800        TCGA-CD-5801        TCGA-CD-5802 
      "4P LOSS CNV" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE"       "4P LOSS CNV" 
       TCGA-CD-5803        TCGA-CG-4300        TCGA-CG-4301        TCGA-CG-4304 
"4P LOSS WILD-TYPE"       "4P LOSS CNV" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" 
       TCGA-CG-4305        TCGA-CG-4306        TCGA-CG-4436        TCGA-CG-4437 
"4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" 
       TCGA-CG-4438        TCGA-CG-4440        TCGA-CG-4441        TCGA-CG-4443 
      "4P LOSS CNV"       "4P LOSS CNV" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" 
       TCGA-CG-4444        TCGA-CG-4449        TCGA-CG-4455        TCGA-CG-4460 
"4P LOSS WILD-TYPE"       "4P LOSS CNV" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" 
       TCGA-CG-4462        TCGA-CG-4465        TCGA-CG-4466        TCGA-CG-4469 
"4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE"       "4P LOSS CNV"       "4P LOSS CNV" 
       TCGA-CG-4472        TCGA-CG-4474        TCGA-CG-4477        TCGA-CG-5716 
"4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE"       "4P LOSS CNV" "4P LOSS WILD-TYPE" 
       TCGA-CG-5717        TCGA-CG-5718        TCGA-CG-5719        TCGA-CG-5720 
"4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" 
       TCGA-CG-5721        TCGA-CG-5722        TCGA-CG-5723        TCGA-CG-5724 
"4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" 
       TCGA-CG-5725        TCGA-CG-5726        TCGA-CG-5727        TCGA-CG-5728 
      "4P LOSS CNV" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" 
       TCGA-CG-5730        TCGA-CG-5732        TCGA-CG-5733        TCGA-CG-5734 
"4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" 
       TCGA-D7-5577        TCGA-D7-5578        TCGA-D7-5579        TCGA-D7-6518 
"4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" 
       TCGA-D7-6519        TCGA-D7-6520        TCGA-D7-6521        TCGA-D7-6522 
      "4P LOSS CNV" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" 
       TCGA-D7-6524        TCGA-D7-6525        TCGA-D7-6526        TCGA-D7-6527 
"4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE"       "4P LOSS CNV" 
       TCGA-D7-6528        TCGA-D7-6815        TCGA-D7-6817        TCGA-D7-6818 
      "4P LOSS CNV" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" 
       TCGA-D7-6820        TCGA-D7-6822        TCGA-EQ-5647        TCGA-EQ-8122 
      "4P LOSS CNV" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE"       "4P LOSS CNV" 
       TCGA-F1-6177        TCGA-F1-6874        TCGA-F1-6875        TCGA-FP-7735 
"4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" 
       TCGA-FP-7829        TCGA-FP-7916        TCGA-FP-7998        TCGA-FP-8099 
"4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE"       "4P LOSS CNV" 
       TCGA-FP-8209        TCGA-FP-8210        TCGA-FP-8631        TCGA-HJ-7597 
"4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE"       "4P LOSS CNV" 
       TCGA-IN-7806        TCGA-IN-7808        TCGA-IP-7968 
"4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" 
       TCGA-B7-5816        TCGA-B7-5818        TCGA-BR-6452        TCGA-BR-6455 
"4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" 
       TCGA-BR-6457        TCGA-BR-6458        TCGA-BR-6563        TCGA-BR-6564 
"4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" 
       TCGA-BR-6565        TCGA-BR-6566        TCGA-BR-6705        TCGA-BR-6706 
"4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" 
       TCGA-BR-6707        TCGA-BR-6709        TCGA-BR-6710        TCGA-BR-6801 
"4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" 
       TCGA-BR-6802        TCGA-BR-6803        TCGA-BR-6852        TCGA-BR-7196 
"4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" 
       TCGA-BR-7197        TCGA-BR-7703        TCGA-BR-7704        TCGA-BR-7707 
      "4P LOSS CNV" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" 
       TCGA-BR-7715        TCGA-BR-7716        TCGA-BR-7717        TCGA-BR-7722 
"4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" 
       TCGA-BR-7723        TCGA-BR-7851        TCGA-BR-7901        TCGA-BR-7957 
      "4P LOSS CNV" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" 
       TCGA-BR-7958        TCGA-BR-7959        TCGA-BR-8059        TCGA-BR-8060 
"4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" 
       TCGA-BR-8077        TCGA-BR-8078        TCGA-BR-8080        TCGA-BR-8081 
"4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" 
       TCGA-BR-8284        TCGA-BR-8285        TCGA-BR-8286        TCGA-BR-8289 
"4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE"       "4P LOSS CNV" 
       TCGA-BR-8291        TCGA-BR-8295        TCGA-BR-8296        TCGA-BR-8297 
      "4P LOSS CNV"       "4P LOSS CNV" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" 
       TCGA-BR-8592        TCGA-BR-A4IU        TCGA-BR-A4IV        TCGA-BR-A4IY 
"4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" 
       TCGA-BR-A4IZ        TCGA-BR-A4J1        TCGA-BR-A4J2        TCGA-BR-A4J4 
"4P LOSS WILD-TYPE"       "4P LOSS CNV" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" 
       TCGA-BR-A4J5        TCGA-BR-A4J6        TCGA-BR-A4J8        TCGA-BR-A4J9 
"4P LOSS WILD-TYPE"       "4P LOSS CNV" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" 
       TCGA-BR-A4PF        TCGA-BR-A4QI        TCGA-BR-A4QL        TCGA-CD-5798 
"4P LOSS WILD-TYPE"       "4P LOSS CNV" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" 
       TCGA-CD-5799        TCGA-CD-5800        TCGA-CD-5801        TCGA-CD-5802 
      "4P LOSS CNV" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE"       "4P LOSS CNV" 
       TCGA-CD-5803        TCGA-CG-4300        TCGA-CG-4301        TCGA-CG-4304 
"4P LOSS WILD-TYPE"       "4P LOSS CNV" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" 
       TCGA-CG-4305        TCGA-CG-4306        TCGA-CG-4436        TCGA-CG-4437 
"4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" 
       TCGA-CG-4438        TCGA-CG-4440        TCGA-CG-4441        TCGA-CG-4443 
      "4P LOSS CNV"       "4P LOSS CNV" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" 
       TCGA-CG-4444        TCGA-CG-4449        TCGA-CG-4455        TCGA-CG-4460 
"4P LOSS WILD-TYPE"       "4P LOSS CNV" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" 
       TCGA-CG-4462        TCGA-CG-4465        TCGA-CG-4466        TCGA-CG-4469 
"4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE"       "4P LOSS CNV"       "4P LOSS CNV" 
       TCGA-CG-4472        TCGA-CG-4474        TCGA-CG-4477        TCGA-CG-5716 
"4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE"       "4P LOSS CNV" "4P LOSS WILD-TYPE" 
       TCGA-CG-5717        TCGA-CG-5718        TCGA-CG-5719        TCGA-CG-5720 
"4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" 
       TCGA-CG-5721        TCGA-CG-5722        TCGA-CG-5723        TCGA-CG-5724 
"4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" 
       TCGA-CG-5725        TCGA-CG-5726        TCGA-CG-5727        TCGA-CG-5728 
      "4P LOSS CNV" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" 
       TCGA-CG-5730        TCGA-CG-5732        TCGA-CG-5733        TCGA-CG-5734 
"4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" 
       TCGA-D7-5577        TCGA-D7-5578        TCGA-D7-5579        TCGA-D7-6518 
"4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" 
       TCGA-D7-6519        TCGA-D7-6520        TCGA-D7-6521        TCGA-D7-6522 
      "4P LOSS CNV" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" 
       TCGA-D7-6524        TCGA-D7-6525        TCGA-D7-6526        TCGA-D7-6527 
"4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE"       "4P LOSS CNV" 
       TCGA-D7-6528        TCGA-D7-6815        TCGA-D7-6817        TCGA-D7-6818 
      "4P LOSS CNV" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" 
       TCGA-D7-6820        TCGA-D7-6822        TCGA-EQ-5647        TCGA-EQ-8122 
      "4P LOSS CNV" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE"       "4P LOSS CNV" 
       TCGA-F1-6177        TCGA-F1-6874        TCGA-F1-6875        TCGA-FP-7735 
"4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" 
       TCGA-FP-7829        TCGA-FP-7916        TCGA-FP-7998        TCGA-FP-8099 
"4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE"       "4P LOSS CNV" 
       TCGA-FP-8209        TCGA-FP-8210        TCGA-FP-8631        TCGA-HJ-7597 
"4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE"       "4P LOSS CNV" 
       TCGA-IN-7806        TCGA-IN-7808        TCGA-IP-7968 
"4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" 
[1] "hr=" "1.5"
D42V2, continuous
D42V3, binary
[1] "tbl2"
                   cls
clus                [,1] [,2]
  4P LOSS CNV         11   19
  4P LOSS WILD-TYPE   61   89
        clus
vv       4P LOSS CNV 4P LOSS WILD-TYPE
  FEMALE          11                61
  MALE            19                89
                   vv
clus                STOMACH  ADENOCARCINOMA  DIFFUSE TYPE
  4P LOSS CNV                                           1
  4P LOSS WILD-TYPE                                     9
                   vv
clus                STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  4P LOSS CNV                                                            5
  4P LOSS WILD-TYPE                                                     11
                   vv
clus                STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  4P LOSS CNV                                                                       2
  4P LOSS WILD-TYPE                                                                 6
                   vv
clus                STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE
  4P LOSS CNV                                                              0
  4P LOSS WILD-TYPE                                                        3
                   vv
clus                STOMACH ADENOCARCINOMA  SIGNET RING TYPE
  4P LOSS CNV                                              1
  4P LOSS WILD-TYPE                                        0
                   vv
clus                STOMACH ADENOCARCINOMA - DIFFUSE TYPE
  4P LOSS CNV                                           1
  4P LOSS WILD-TYPE                                    15
                   vv
clus                STOMACH ADENOCARCINOMA - NOT OTHERWISE SPECIFIED (NOS)
  4P LOSS CNV                                                            8
  4P LOSS WILD-TYPE                                                     65
                   vv
clus                STOMACH INTESTINAL ADENOCARCINOMA - MUCINOUS TYPE
  4P LOSS CNV                                                       2
  4P LOSS WILD-TYPE                                                 5
                   vv
clus                STOMACH INTESTINAL ADENOCARCINOMA - PAPILLARY TYPE
  4P LOSS CNV                                                        1
  4P LOSS WILD-TYPE                                                  2
                   vv
clus                STOMACH INTESTINAL ADENOCARCINOMA - TUBULAR TYPE
  4P LOSS CNV                                                      3
  4P LOSS WILD-TYPE                                                7
                   vv
clus                STOMACH INTESTINAL ADENOCARCINOMA - TYPE NOT OTHERWISE SPECIFIED (NOS)
  4P LOSS CNV                                                                            6
  4P LOSS WILD-TYPE                                                                     22
D42V4, multiclass
                   vv
clus                T1 T2 T3 T4
  4P LOSS CNV        0 12  8  1
  4P LOSS WILD-TYPE  6 40 48 17
D42V5, multiclass
    clus
vv   4P LOSS CNV 4P LOSS WILD-TYPE
  T1           0                 6
  T2          12                40
  T3           8                48
  T4           1                17
                   vv
clus                N0 N1 N2 N3
  4P LOSS CNV        7  7  3  3
  4P LOSS WILD-TYPE 37 42 20 12
D42V6, multiclass
    clus
vv   4P LOSS CNV 4P LOSS WILD-TYPE
  N0           7                37
  N1           7                42
  N2           3                20
  N3           3                12
                   vv
clus                M0 M1 MX
  4P LOSS CNV       20  1  0
  4P LOSS WILD-TYPE 98 15  8
D42V7, multiclass
    clus
vv   4P LOSS CNV 4P LOSS WILD-TYPE
  M0          20                98
  M1           1                15
  MX           0                 8
                   vv
clus                 I II III IV
  4P LOSS CNV        4  9   3  4
  4P LOSS WILD-TYPE 20 28  36 22
D42V8, multiclass
     clus
vv    4P LOSS CNV 4P LOSS WILD-TYPE
  I             4                20
  II            9                28
  III           3                36
  IV            4                22
D42V9, binary
[1] "tbl2"
                   cls
clus                [,1] [,2]
  4P LOSS CNV          2   28
  4P LOSS WILD-TYPE    3  147
     clus
vv    4P LOSS CNV 4P LOSS WILD-TYPE
  NO            2                 3
  YES          28               147
                   vv
clus                 R0  R1  R2  RX
  4P LOSS CNV        21   3   1   2
  4P LOSS WILD-TYPE 104   4  11  23
D42V10, multiclass
    clus
vv   4P LOSS CNV 4P LOSS WILD-TYPE
  R0          21               104
  R1           3                 4
  R2           1                11
  RX           2                23
D42V11, continuous

Clustering(43) Variable = 4q loss
D43V1, survival
                   sevent
clus2                 0   1
  4Q LOSS CNV        22   3
  4Q LOSS WILD-TYPE 102  16
      4Q LOSS CNV 4Q LOSS WILD-TYPE 
               25               118 
      4Q LOSS CNV 4Q LOSS WILD-TYPE 
                3                16 
$`4Q LOSS CNV`
TCGA-BR-6458 TCGA-BR-7723 TCGA-BR-8291 TCGA-BR-8295 TCGA-BR-A4J1 TCGA-BR-A4J6 
        1.35         4.54         1.18         1.55         0.72         0.13 
TCGA-BR-A4PF TCGA-BR-A4QI TCGA-CD-5799 TCGA-CD-5802 TCGA-CG-4300 TCGA-CG-4438 
        0.72         0.49         0.69         0.30        20.02        54.05 
TCGA-CG-4440 TCGA-CG-4449 TCGA-CG-4466 TCGA-CG-4477 TCGA-CG-5725 TCGA-CG-5730 
        4.01        19.07        18.94         1.02        15.02         4.01 
TCGA-D7-6519 TCGA-D7-6527 TCGA-D7-6528 TCGA-D7-6815 TCGA-D7-6820 TCGA-EQ-8122 
       15.65         4.14         1.68         3.65         2.93         7.79 
TCGA-FP-8099 
        1.02 

$`4Q LOSS WILD-TYPE`
TCGA-B7-5816 TCGA-B7-5818 TCGA-BR-6452 TCGA-BR-6455 TCGA-BR-6457 TCGA-BR-6563 
        5.62         0.10         0.95         1.41         1.35         0.85 
TCGA-BR-6564 TCGA-BR-6565 TCGA-BR-6566 TCGA-BR-6705 TCGA-BR-6706 TCGA-BR-6707 
        0.82         0.62         0.62         1.71         2.17         0.99 
TCGA-BR-6709 TCGA-BR-6710 TCGA-BR-6801 TCGA-BR-6802 TCGA-BR-6803 TCGA-BR-6852 
        1.22         0.66         1.12         0.76         0.66         0.26 
TCGA-BR-7196 TCGA-BR-7197 TCGA-BR-7703 TCGA-BR-7704 TCGA-BR-7707 TCGA-BR-7715 
        1.22         1.48         0.46         1.25         0.13         1.05 
TCGA-BR-7716 TCGA-BR-7717 TCGA-BR-7722 TCGA-BR-7851 TCGA-BR-7901 TCGA-BR-7957 
        0.82         0.69         0.16         0.99         0.95         0.69 
TCGA-BR-7958 TCGA-BR-7959 TCGA-BR-8059 TCGA-BR-8060 TCGA-BR-8077 TCGA-BR-8078 
        0.16         1.08         0.82         1.32         0.69         0.95 
TCGA-BR-8080 TCGA-BR-8081 TCGA-BR-8284 TCGA-BR-8285 TCGA-BR-8286 TCGA-BR-8289 
        0.49         0.46         0.72         0.26         0.43         0.26 
TCGA-BR-8296 TCGA-BR-8297 TCGA-BR-8592 TCGA-BR-A4IU TCGA-BR-A4IV TCGA-BR-A4IY 
        1.48         0.76         0.20         0.59         0.92         0.39 
TCGA-BR-A4IZ TCGA-BR-A4J2 TCGA-BR-A4J4 TCGA-BR-A4J5 TCGA-BR-A4J8 TCGA-BR-A4J9 
        0.79         0.79         0.53         0.43         0.23         0.10 
TCGA-BR-A4QL TCGA-CD-5798 TCGA-CD-5800 TCGA-CD-5801 TCGA-CD-5803 TCGA-CG-4301 
        2.24         0.82         0.36         0.49         0.07         3.02 
TCGA-CG-4304 TCGA-CG-4305 TCGA-CG-4306 TCGA-CG-4436 TCGA-CG-4437 TCGA-CG-4441 
       27.02        15.95         1.02        52.96         8.05        14.01 
TCGA-CG-4443 TCGA-CG-4444 TCGA-CG-4455 TCGA-CG-4460 TCGA-CG-4462 TCGA-CG-4465 
       29.98        47.05        12.03        21.99         1.02         8.98 
TCGA-CG-4469 TCGA-CG-4472 TCGA-CG-4474 TCGA-CG-5716 TCGA-CG-5717 TCGA-CG-5718 
        7.07        12.00         1.02         1.02         6.94         1.02 
TCGA-CG-5719 TCGA-CG-5720 TCGA-CG-5721 TCGA-CG-5722 TCGA-CG-5723 TCGA-CG-5724 
        1.02         0.99         5.98         0.95        70.06        12.03 
TCGA-CG-5726 TCGA-CG-5727 TCGA-CG-5728 TCGA-CG-5732 TCGA-CG-5733 TCGA-CG-5734 
       28.96        31.04        65.10        55.04        21.07         7.99 
TCGA-D7-5577 TCGA-D7-5578 TCGA-D7-5579 TCGA-D7-6518 TCGA-D7-6520 TCGA-D7-6521 
        8.65         3.58         4.54         9.80         9.63         8.19 
TCGA-D7-6522 TCGA-D7-6524 TCGA-D7-6525 TCGA-D7-6526 TCGA-D7-6817 TCGA-D7-6818 
        6.90         0.69         5.95         6.61         4.70         4.04 
TCGA-D7-6822 TCGA-EQ-5647 TCGA-F1-6177 TCGA-F1-6874 TCGA-F1-6875 TCGA-FP-7735 
        4.27         0.62         6.54         2.01        72.23         0.39 
TCGA-FP-7829 TCGA-FP-7916 TCGA-FP-7998 TCGA-FP-8209 TCGA-FP-8210 TCGA-FP-8631 
        0.20         3.02         3.58        59.05         5.03         0.56 
TCGA-HJ-7597 TCGA-IN-7806 TCGA-IN-7808 TCGA-IP-7968 
       26.43         6.87         3.55         2.53 

      4Q LOSS CNV 4Q LOSS WILD-TYPE 
             0.13              0.07 
      4Q LOSS CNV 4Q LOSS WILD-TYPE 
            54.05             72.23 
      4Q LOSS CNV 4Q LOSS WILD-TYPE 
             2.93              1.10 
[1] "0.1 - 54.0 (2.9)" "0.1 - 72.2 (1.1)"
       TCGA-B7-5816        TCGA-B7-5818        TCGA-BR-6452        TCGA-BR-6455 
"4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" 
       TCGA-BR-6457        TCGA-BR-6458        TCGA-BR-6563        TCGA-BR-6564 
"4Q LOSS WILD-TYPE"       "4Q LOSS CNV" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" 
       TCGA-BR-6565        TCGA-BR-6566        TCGA-BR-6705        TCGA-BR-6706 
"4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" 
       TCGA-BR-6707        TCGA-BR-6709        TCGA-BR-6710        TCGA-BR-6801 
"4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" 
       TCGA-BR-6802        TCGA-BR-6803        TCGA-BR-6852        TCGA-BR-7196 
"4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" 
       TCGA-BR-7197        TCGA-BR-7703        TCGA-BR-7704        TCGA-BR-7707 
"4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" 
       TCGA-BR-7715        TCGA-BR-7716        TCGA-BR-7717        TCGA-BR-7722 
"4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" 
       TCGA-BR-7723        TCGA-BR-7851        TCGA-BR-7901        TCGA-BR-7957 
      "4Q LOSS CNV" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" 
       TCGA-BR-7958        TCGA-BR-7959        TCGA-BR-8059        TCGA-BR-8060 
"4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" 
       TCGA-BR-8077        TCGA-BR-8078        TCGA-BR-8080        TCGA-BR-8081 
"4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" 
       TCGA-BR-8284        TCGA-BR-8285        TCGA-BR-8286        TCGA-BR-8289 
"4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" 
       TCGA-BR-8291        TCGA-BR-8295        TCGA-BR-8296        TCGA-BR-8297 
      "4Q LOSS CNV"       "4Q LOSS CNV" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" 
       TCGA-BR-8592        TCGA-BR-A4IU        TCGA-BR-A4IV        TCGA-BR-A4IY 
"4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" 
       TCGA-BR-A4IZ        TCGA-BR-A4J1        TCGA-BR-A4J2        TCGA-BR-A4J4 
"4Q LOSS WILD-TYPE"       "4Q LOSS CNV" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" 
       TCGA-BR-A4J5        TCGA-BR-A4J6        TCGA-BR-A4J8        TCGA-BR-A4J9 
"4Q LOSS WILD-TYPE"       "4Q LOSS CNV" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" 
       TCGA-BR-A4PF        TCGA-BR-A4QI        TCGA-BR-A4QL        TCGA-CD-5798 
      "4Q LOSS CNV"       "4Q LOSS CNV" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" 
       TCGA-CD-5799        TCGA-CD-5800        TCGA-CD-5801        TCGA-CD-5802 
      "4Q LOSS CNV" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE"       "4Q LOSS CNV" 
       TCGA-CD-5803        TCGA-CG-4300        TCGA-CG-4301        TCGA-CG-4304 
"4Q LOSS WILD-TYPE"       "4Q LOSS CNV" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" 
       TCGA-CG-4305        TCGA-CG-4306        TCGA-CG-4436        TCGA-CG-4437 
"4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" 
       TCGA-CG-4438        TCGA-CG-4440        TCGA-CG-4441        TCGA-CG-4443 
      "4Q LOSS CNV"       "4Q LOSS CNV" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" 
       TCGA-CG-4444        TCGA-CG-4449        TCGA-CG-4455        TCGA-CG-4460 
"4Q LOSS WILD-TYPE"       "4Q LOSS CNV" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" 
       TCGA-CG-4462        TCGA-CG-4465        TCGA-CG-4466        TCGA-CG-4469 
"4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE"       "4Q LOSS CNV" "4Q LOSS WILD-TYPE" 
       TCGA-CG-4472        TCGA-CG-4474        TCGA-CG-4477        TCGA-CG-5716 
"4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE"       "4Q LOSS CNV" "4Q LOSS WILD-TYPE" 
       TCGA-CG-5717        TCGA-CG-5718        TCGA-CG-5719        TCGA-CG-5720 
"4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" 
       TCGA-CG-5721        TCGA-CG-5722        TCGA-CG-5723        TCGA-CG-5724 
"4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" 
       TCGA-CG-5725        TCGA-CG-5726        TCGA-CG-5727        TCGA-CG-5728 
      "4Q LOSS CNV" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" 
       TCGA-CG-5730        TCGA-CG-5732        TCGA-CG-5733        TCGA-CG-5734 
      "4Q LOSS CNV" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" 
       TCGA-D7-5577        TCGA-D7-5578        TCGA-D7-5579        TCGA-D7-6518 
"4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" 
       TCGA-D7-6519        TCGA-D7-6520        TCGA-D7-6521        TCGA-D7-6522 
      "4Q LOSS CNV" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" 
       TCGA-D7-6524        TCGA-D7-6525        TCGA-D7-6526        TCGA-D7-6527 
"4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE"       "4Q LOSS CNV" 
       TCGA-D7-6528        TCGA-D7-6815        TCGA-D7-6817        TCGA-D7-6818 
      "4Q LOSS CNV"       "4Q LOSS CNV" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" 
       TCGA-D7-6820        TCGA-D7-6822        TCGA-EQ-5647        TCGA-EQ-8122 
      "4Q LOSS CNV" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE"       "4Q LOSS CNV" 
       TCGA-F1-6177        TCGA-F1-6874        TCGA-F1-6875        TCGA-FP-7735 
"4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" 
       TCGA-FP-7829        TCGA-FP-7916        TCGA-FP-7998        TCGA-FP-8099 
"4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE"       "4Q LOSS CNV" 
       TCGA-FP-8209        TCGA-FP-8210        TCGA-FP-8631        TCGA-HJ-7597 
"4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" 
       TCGA-IN-7806        TCGA-IN-7808        TCGA-IP-7968 
"4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" 
       TCGA-B7-5816        TCGA-B7-5818        TCGA-BR-6452        TCGA-BR-6455 
"4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" 
       TCGA-BR-6457        TCGA-BR-6458        TCGA-BR-6563        TCGA-BR-6564 
"4Q LOSS WILD-TYPE"       "4Q LOSS CNV" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" 
       TCGA-BR-6565        TCGA-BR-6566        TCGA-BR-6705        TCGA-BR-6706 
"4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" 
       TCGA-BR-6707        TCGA-BR-6709        TCGA-BR-6710        TCGA-BR-6801 
"4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" 
       TCGA-BR-6802        TCGA-BR-6803        TCGA-BR-6852        TCGA-BR-7196 
"4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" 
       TCGA-BR-7197        TCGA-BR-7703        TCGA-BR-7704        TCGA-BR-7707 
"4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" 
       TCGA-BR-7715        TCGA-BR-7716        TCGA-BR-7717        TCGA-BR-7722 
"4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" 
       TCGA-BR-7723        TCGA-BR-7851        TCGA-BR-7901        TCGA-BR-7957 
      "4Q LOSS CNV" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" 
       TCGA-BR-7958        TCGA-BR-7959        TCGA-BR-8059        TCGA-BR-8060 
"4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" 
       TCGA-BR-8077        TCGA-BR-8078        TCGA-BR-8080        TCGA-BR-8081 
"4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" 
       TCGA-BR-8284        TCGA-BR-8285        TCGA-BR-8286        TCGA-BR-8289 
"4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" 
       TCGA-BR-8291        TCGA-BR-8295        TCGA-BR-8296        TCGA-BR-8297 
      "4Q LOSS CNV"       "4Q LOSS CNV" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" 
       TCGA-BR-8592        TCGA-BR-A4IU        TCGA-BR-A4IV        TCGA-BR-A4IY 
"4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" 
       TCGA-BR-A4IZ        TCGA-BR-A4J1        TCGA-BR-A4J2        TCGA-BR-A4J4 
"4Q LOSS WILD-TYPE"       "4Q LOSS CNV" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" 
       TCGA-BR-A4J5        TCGA-BR-A4J6        TCGA-BR-A4J8        TCGA-BR-A4J9 
"4Q LOSS WILD-TYPE"       "4Q LOSS CNV" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" 
       TCGA-BR-A4PF        TCGA-BR-A4QI        TCGA-BR-A4QL        TCGA-CD-5798 
      "4Q LOSS CNV"       "4Q LOSS CNV" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" 
       TCGA-CD-5799        TCGA-CD-5800        TCGA-CD-5801        TCGA-CD-5802 
      "4Q LOSS CNV" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE"       "4Q LOSS CNV" 
       TCGA-CD-5803        TCGA-CG-4300        TCGA-CG-4301        TCGA-CG-4304 
"4Q LOSS WILD-TYPE"       "4Q LOSS CNV" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" 
       TCGA-CG-4305        TCGA-CG-4306        TCGA-CG-4436        TCGA-CG-4437 
"4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" 
       TCGA-CG-4438        TCGA-CG-4440        TCGA-CG-4441        TCGA-CG-4443 
      "4Q LOSS CNV"       "4Q LOSS CNV" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" 
       TCGA-CG-4444        TCGA-CG-4449        TCGA-CG-4455        TCGA-CG-4460 
"4Q LOSS WILD-TYPE"       "4Q LOSS CNV" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" 
       TCGA-CG-4462        TCGA-CG-4465        TCGA-CG-4466        TCGA-CG-4469 
"4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE"       "4Q LOSS CNV" "4Q LOSS WILD-TYPE" 
       TCGA-CG-4472        TCGA-CG-4474        TCGA-CG-4477        TCGA-CG-5716 
"4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE"       "4Q LOSS CNV" "4Q LOSS WILD-TYPE" 
       TCGA-CG-5717        TCGA-CG-5718        TCGA-CG-5719        TCGA-CG-5720 
"4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" 
       TCGA-CG-5721        TCGA-CG-5722        TCGA-CG-5723        TCGA-CG-5724 
"4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" 
       TCGA-CG-5725        TCGA-CG-5726        TCGA-CG-5727        TCGA-CG-5728 
      "4Q LOSS CNV" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" 
       TCGA-CG-5730        TCGA-CG-5732        TCGA-CG-5733        TCGA-CG-5734 
      "4Q LOSS CNV" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" 
       TCGA-D7-5577        TCGA-D7-5578        TCGA-D7-5579        TCGA-D7-6518 
"4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" 
       TCGA-D7-6519        TCGA-D7-6520        TCGA-D7-6521        TCGA-D7-6522 
      "4Q LOSS CNV" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" 
       TCGA-D7-6524        TCGA-D7-6525        TCGA-D7-6526        TCGA-D7-6527 
"4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE"       "4Q LOSS CNV" 
       TCGA-D7-6528        TCGA-D7-6815        TCGA-D7-6817        TCGA-D7-6818 
      "4Q LOSS CNV"       "4Q LOSS CNV" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" 
       TCGA-D7-6820        TCGA-D7-6822        TCGA-EQ-5647        TCGA-EQ-8122 
      "4Q LOSS CNV" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE"       "4Q LOSS CNV" 
       TCGA-F1-6177        TCGA-F1-6874        TCGA-F1-6875        TCGA-FP-7735 
"4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" 
       TCGA-FP-7829        TCGA-FP-7916        TCGA-FP-7998        TCGA-FP-8099 
"4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE"       "4Q LOSS CNV" 
       TCGA-FP-8209        TCGA-FP-8210        TCGA-FP-8631        TCGA-HJ-7597 
"4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" 
       TCGA-IN-7806        TCGA-IN-7808        TCGA-IP-7968 
"4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" 
       TCGA-B7-5816        TCGA-B7-5818        TCGA-BR-6452        TCGA-BR-6455 
"4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" 
       TCGA-BR-6457        TCGA-BR-6458        TCGA-BR-6563        TCGA-BR-6564 
"4Q LOSS WILD-TYPE"       "4Q LOSS CNV" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" 
       TCGA-BR-6565        TCGA-BR-6566        TCGA-BR-6705        TCGA-BR-6706 
"4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" 
       TCGA-BR-6707        TCGA-BR-6709        TCGA-BR-6710        TCGA-BR-6801 
"4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" 
       TCGA-BR-6802        TCGA-BR-6803        TCGA-BR-6852        TCGA-BR-7196 
"4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" 
       TCGA-BR-7197        TCGA-BR-7703        TCGA-BR-7704        TCGA-BR-7707 
"4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" 
       TCGA-BR-7715        TCGA-BR-7716        TCGA-BR-7717        TCGA-BR-7722 
"4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" 
       TCGA-BR-7723        TCGA-BR-7851        TCGA-BR-7901        TCGA-BR-7957 
      "4Q LOSS CNV" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" 
       TCGA-BR-7958        TCGA-BR-7959        TCGA-BR-8059        TCGA-BR-8060 
"4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" 
       TCGA-BR-8077        TCGA-BR-8078        TCGA-BR-8080        TCGA-BR-8081 
"4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" 
       TCGA-BR-8284        TCGA-BR-8285        TCGA-BR-8286        TCGA-BR-8289 
"4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" 
       TCGA-BR-8291        TCGA-BR-8295        TCGA-BR-8296        TCGA-BR-8297 
      "4Q LOSS CNV"       "4Q LOSS CNV" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" 
       TCGA-BR-8592        TCGA-BR-A4IU        TCGA-BR-A4IV        TCGA-BR-A4IY 
"4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" 
       TCGA-BR-A4IZ        TCGA-BR-A4J1        TCGA-BR-A4J2        TCGA-BR-A4J4 
"4Q LOSS WILD-TYPE"       "4Q LOSS CNV" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" 
       TCGA-BR-A4J5        TCGA-BR-A4J6        TCGA-BR-A4J8        TCGA-BR-A4J9 
"4Q LOSS WILD-TYPE"       "4Q LOSS CNV" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" 
       TCGA-BR-A4PF        TCGA-BR-A4QI        TCGA-BR-A4QL        TCGA-CD-5798 
      "4Q LOSS CNV"       "4Q LOSS CNV" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" 
       TCGA-CD-5799        TCGA-CD-5800        TCGA-CD-5801        TCGA-CD-5802 
      "4Q LOSS CNV" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE"       "4Q LOSS CNV" 
       TCGA-CD-5803        TCGA-CG-4300        TCGA-CG-4301        TCGA-CG-4304 
"4Q LOSS WILD-TYPE"       "4Q LOSS CNV" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" 
       TCGA-CG-4305        TCGA-CG-4306        TCGA-CG-4436        TCGA-CG-4437 
"4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" 
       TCGA-CG-4438        TCGA-CG-4440        TCGA-CG-4441        TCGA-CG-4443 
      "4Q LOSS CNV"       "4Q LOSS CNV" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" 
       TCGA-CG-4444        TCGA-CG-4449        TCGA-CG-4455        TCGA-CG-4460 
"4Q LOSS WILD-TYPE"       "4Q LOSS CNV" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" 
       TCGA-CG-4462        TCGA-CG-4465        TCGA-CG-4466        TCGA-CG-4469 
"4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE"       "4Q LOSS CNV" "4Q LOSS WILD-TYPE" 
       TCGA-CG-4472        TCGA-CG-4474        TCGA-CG-4477        TCGA-CG-5716 
"4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE"       "4Q LOSS CNV" "4Q LOSS WILD-TYPE" 
       TCGA-CG-5717        TCGA-CG-5718        TCGA-CG-5719        TCGA-CG-5720 
"4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" 
       TCGA-CG-5721        TCGA-CG-5722        TCGA-CG-5723        TCGA-CG-5724 
"4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" 
       TCGA-CG-5725        TCGA-CG-5726        TCGA-CG-5727        TCGA-CG-5728 
      "4Q LOSS CNV" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" 
       TCGA-CG-5730        TCGA-CG-5732        TCGA-CG-5733        TCGA-CG-5734 
      "4Q LOSS CNV" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" 
       TCGA-D7-5577        TCGA-D7-5578        TCGA-D7-5579        TCGA-D7-6518 
"4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" 
       TCGA-D7-6519        TCGA-D7-6520        TCGA-D7-6521        TCGA-D7-6522 
      "4Q LOSS CNV" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" 
       TCGA-D7-6524        TCGA-D7-6525        TCGA-D7-6526        TCGA-D7-6527 
"4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE"       "4Q LOSS CNV" 
       TCGA-D7-6528        TCGA-D7-6815        TCGA-D7-6817        TCGA-D7-6818 
      "4Q LOSS CNV"       "4Q LOSS CNV" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" 
       TCGA-D7-6820        TCGA-D7-6822        TCGA-EQ-5647        TCGA-EQ-8122 
      "4Q LOSS CNV" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE"       "4Q LOSS CNV" 
       TCGA-F1-6177        TCGA-F1-6874        TCGA-F1-6875        TCGA-FP-7735 
"4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" 
       TCGA-FP-7829        TCGA-FP-7916        TCGA-FP-7998        TCGA-FP-8099 
"4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE"       "4Q LOSS CNV" 
       TCGA-FP-8209        TCGA-FP-8210        TCGA-FP-8631        TCGA-HJ-7597 
"4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" 
       TCGA-IN-7806        TCGA-IN-7808        TCGA-IP-7968 
"4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" 
[1] "hr=" "1.1"
D43V2, continuous
D43V3, binary
[1] "tbl2"
                   cls
clus                [,1] [,2]
  4Q LOSS CNV         13   15
  4Q LOSS WILD-TYPE   59   93
        clus
vv       4Q LOSS CNV 4Q LOSS WILD-TYPE
  FEMALE          13                59
  MALE            15                93
                   vv
clus                STOMACH  ADENOCARCINOMA  DIFFUSE TYPE
  4Q LOSS CNV                                           1
  4Q LOSS WILD-TYPE                                     9
                   vv
clus                STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  4Q LOSS CNV                                                            6
  4Q LOSS WILD-TYPE                                                     10
                   vv
clus                STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  4Q LOSS CNV                                                                       1
  4Q LOSS WILD-TYPE                                                                 7
                   vv
clus                STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE
  4Q LOSS CNV                                                              0
  4Q LOSS WILD-TYPE                                                        3
                   vv
clus                STOMACH ADENOCARCINOMA  SIGNET RING TYPE
  4Q LOSS CNV                                              0
  4Q LOSS WILD-TYPE                                        1
                   vv
clus                STOMACH ADENOCARCINOMA - DIFFUSE TYPE
  4Q LOSS CNV                                           1
  4Q LOSS WILD-TYPE                                    15
                   vv
clus                STOMACH ADENOCARCINOMA - NOT OTHERWISE SPECIFIED (NOS)
  4Q LOSS CNV                                                            6
  4Q LOSS WILD-TYPE                                                     67
                   vv
clus                STOMACH INTESTINAL ADENOCARCINOMA - MUCINOUS TYPE
  4Q LOSS CNV                                                       2
  4Q LOSS WILD-TYPE                                                 5
                   vv
clus                STOMACH INTESTINAL ADENOCARCINOMA - PAPILLARY TYPE
  4Q LOSS CNV                                                        1
  4Q LOSS WILD-TYPE                                                  2
                   vv
clus                STOMACH INTESTINAL ADENOCARCINOMA - TUBULAR TYPE
  4Q LOSS CNV                                                      4
  4Q LOSS WILD-TYPE                                                6
                   vv
clus                STOMACH INTESTINAL ADENOCARCINOMA - TYPE NOT OTHERWISE SPECIFIED (NOS)
  4Q LOSS CNV                                                                            6
  4Q LOSS WILD-TYPE                                                                     22
D43V4, multiclass
                   vv
clus                T1 T2 T3 T4
  4Q LOSS CNV        0 13  6  1
  4Q LOSS WILD-TYPE  6 39 50 17
D43V5, multiclass
    clus
vv   4Q LOSS CNV 4Q LOSS WILD-TYPE
  T1           0                 6
  T2          13                39
  T3           6                50
  T4           1                17
                   vv
clus                N0 N1 N2 N3
  4Q LOSS CNV        5  8  4  2
  4Q LOSS WILD-TYPE 39 41 19 13
D43V6, multiclass
    clus
vv   4Q LOSS CNV 4Q LOSS WILD-TYPE
  N0           5                39
  N1           8                41
  N2           4                19
  N3           2                13
                   vv
clus                 M0  M1  MX
  4Q LOSS CNV        18   2   0
  4Q LOSS WILD-TYPE 100  14   8
D43V7, multiclass
    clus
vv   4Q LOSS CNV 4Q LOSS WILD-TYPE
  M0          18               100
  M1           2                14
  MX           0                 8
                   vv
clus                 I II III IV
  4Q LOSS CNV        4  7   4  4
  4Q LOSS WILD-TYPE 20 30  35 22
D43V8, multiclass
     clus
vv    4Q LOSS CNV 4Q LOSS WILD-TYPE
  I             4                20
  II            7                30
  III           4                35
  IV            4                22
D43V9, binary
[1] "tbl2"
                   cls
clus                [,1] [,2]
  4Q LOSS CNV          2   26
  4Q LOSS WILD-TYPE    3  149
     clus
vv    4Q LOSS CNV 4Q LOSS WILD-TYPE
  NO            2                 3
  YES          26               149
                   vv
clus                 R0  R1  R2  RX
  4Q LOSS CNV        20   2   2   1
  4Q LOSS WILD-TYPE 105   5  10  24
D43V10, multiclass
    clus
vv   4Q LOSS CNV 4Q LOSS WILD-TYPE
  R0          20               105
  R1           2                 5
  R2           2                10
  RX           1                24
D43V11, continuous

Clustering(44) Variable = 5p loss
D44V1, survival
                   sevent
clus2                 0   1
  5P LOSS CNV         8   1
  5P LOSS WILD-TYPE 116  18
      5P LOSS CNV 5P LOSS WILD-TYPE 
                9               134 
      5P LOSS CNV 5P LOSS WILD-TYPE 
                1                18 
$`5P LOSS CNV`
TCGA-BR-6458 TCGA-BR-7959 TCGA-BR-8295 TCGA-BR-A4J1 TCGA-CG-4449 TCGA-D7-6520 
        1.35         1.08         1.55         0.72        19.07         9.63 
TCGA-D7-6815 TCGA-FP-8631 TCGA-IN-7806 
        3.65         0.56         6.87 

$`5P LOSS WILD-TYPE`
TCGA-B7-5816 TCGA-B7-5818 TCGA-BR-6452 TCGA-BR-6455 TCGA-BR-6457 TCGA-BR-6563 
        5.62         0.10         0.95         1.41         1.35         0.85 
TCGA-BR-6564 TCGA-BR-6565 TCGA-BR-6566 TCGA-BR-6705 TCGA-BR-6706 TCGA-BR-6707 
        0.82         0.62         0.62         1.71         2.17         0.99 
TCGA-BR-6709 TCGA-BR-6710 TCGA-BR-6801 TCGA-BR-6802 TCGA-BR-6803 TCGA-BR-6852 
        1.22         0.66         1.12         0.76         0.66         0.26 
TCGA-BR-7196 TCGA-BR-7197 TCGA-BR-7703 TCGA-BR-7704 TCGA-BR-7707 TCGA-BR-7715 
        1.22         1.48         0.46         1.25         0.13         1.05 
TCGA-BR-7716 TCGA-BR-7717 TCGA-BR-7722 TCGA-BR-7723 TCGA-BR-7851 TCGA-BR-7901 
        0.82         0.69         0.16         4.54         0.99         0.95 
TCGA-BR-7957 TCGA-BR-7958 TCGA-BR-8059 TCGA-BR-8060 TCGA-BR-8077 TCGA-BR-8078 
        0.69         0.16         0.82         1.32         0.69         0.95 
TCGA-BR-8080 TCGA-BR-8081 TCGA-BR-8284 TCGA-BR-8285 TCGA-BR-8286 TCGA-BR-8289 
        0.49         0.46         0.72         0.26         0.43         0.26 
TCGA-BR-8291 TCGA-BR-8296 TCGA-BR-8297 TCGA-BR-8592 TCGA-BR-A4IU TCGA-BR-A4IV 
        1.18         1.48         0.76         0.20         0.59         0.92 
TCGA-BR-A4IY TCGA-BR-A4IZ TCGA-BR-A4J2 TCGA-BR-A4J4 TCGA-BR-A4J5 TCGA-BR-A4J6 
        0.39         0.79         0.79         0.53         0.43         0.13 
TCGA-BR-A4J8 TCGA-BR-A4J9 TCGA-BR-A4PF TCGA-BR-A4QI TCGA-BR-A4QL TCGA-CD-5798 
        0.23         0.10         0.72         0.49         2.24         0.82 
TCGA-CD-5799 TCGA-CD-5800 TCGA-CD-5801 TCGA-CD-5802 TCGA-CD-5803 TCGA-CG-4300 
        0.69         0.36         0.49         0.30         0.07        20.02 
TCGA-CG-4301 TCGA-CG-4304 TCGA-CG-4305 TCGA-CG-4306 TCGA-CG-4436 TCGA-CG-4437 
        3.02        27.02        15.95         1.02        52.96         8.05 
TCGA-CG-4438 TCGA-CG-4440 TCGA-CG-4441 TCGA-CG-4443 TCGA-CG-4444 TCGA-CG-4455 
       54.05         4.01        14.01        29.98        47.05        12.03 
TCGA-CG-4460 TCGA-CG-4462 TCGA-CG-4465 TCGA-CG-4466 TCGA-CG-4469 TCGA-CG-4472 
       21.99         1.02         8.98        18.94         7.07        12.00 
TCGA-CG-4474 TCGA-CG-4477 TCGA-CG-5716 TCGA-CG-5717 TCGA-CG-5718 TCGA-CG-5719 
        1.02         1.02         1.02         6.94         1.02         1.02 
TCGA-CG-5720 TCGA-CG-5721 TCGA-CG-5722 TCGA-CG-5723 TCGA-CG-5724 TCGA-CG-5725 
        0.99         5.98         0.95        70.06        12.03        15.02 
TCGA-CG-5726 TCGA-CG-5727 TCGA-CG-5728 TCGA-CG-5730 TCGA-CG-5732 TCGA-CG-5733 
       28.96        31.04        65.10         4.01        55.04        21.07 
TCGA-CG-5734 TCGA-D7-5577 TCGA-D7-5578 TCGA-D7-5579 TCGA-D7-6518 TCGA-D7-6519 
        7.99         8.65         3.58         4.54         9.80        15.65 
TCGA-D7-6521 TCGA-D7-6522 TCGA-D7-6524 TCGA-D7-6525 TCGA-D7-6526 TCGA-D7-6527 
        8.19         6.90         0.69         5.95         6.61         4.14 
TCGA-D7-6528 TCGA-D7-6817 TCGA-D7-6818 TCGA-D7-6820 TCGA-D7-6822 TCGA-EQ-5647 
        1.68         4.70         4.04         2.93         4.27         0.62 
TCGA-EQ-8122 TCGA-F1-6177 TCGA-F1-6874 TCGA-F1-6875 TCGA-FP-7735 TCGA-FP-7829 
        7.79         6.54         2.01        72.23         0.39         0.20 
TCGA-FP-7916 TCGA-FP-7998 TCGA-FP-8099 TCGA-FP-8209 TCGA-FP-8210 TCGA-HJ-7597 
        3.02         3.58         1.02        59.05         5.03        26.43 
TCGA-IN-7808 TCGA-IP-7968 
        3.55         2.53 

      5P LOSS CNV 5P LOSS WILD-TYPE 
             0.56              0.07 
      5P LOSS CNV 5P LOSS WILD-TYPE 
            19.07             72.23 
      5P LOSS CNV 5P LOSS WILD-TYPE 
             1.55              1.22 
[1] "0.6 - 19.1 (1.6)" "0.1 - 72.2 (1.2)"
       TCGA-B7-5816        TCGA-B7-5818        TCGA-BR-6452        TCGA-BR-6455 
"5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" 
       TCGA-BR-6457        TCGA-BR-6458        TCGA-BR-6563        TCGA-BR-6564 
"5P LOSS WILD-TYPE"       "5P LOSS CNV" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" 
       TCGA-BR-6565        TCGA-BR-6566        TCGA-BR-6705        TCGA-BR-6706 
"5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" 
       TCGA-BR-6707        TCGA-BR-6709        TCGA-BR-6710        TCGA-BR-6801 
"5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" 
       TCGA-BR-6802        TCGA-BR-6803        TCGA-BR-6852        TCGA-BR-7196 
"5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" 
       TCGA-BR-7197        TCGA-BR-7703        TCGA-BR-7704        TCGA-BR-7707 
"5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" 
       TCGA-BR-7715        TCGA-BR-7716        TCGA-BR-7717        TCGA-BR-7722 
"5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" 
       TCGA-BR-7723        TCGA-BR-7851        TCGA-BR-7901        TCGA-BR-7957 
"5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" 
       TCGA-BR-7958        TCGA-BR-7959        TCGA-BR-8059        TCGA-BR-8060 
"5P LOSS WILD-TYPE"       "5P LOSS CNV" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" 
       TCGA-BR-8077        TCGA-BR-8078        TCGA-BR-8080        TCGA-BR-8081 
"5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" 
       TCGA-BR-8284        TCGA-BR-8285        TCGA-BR-8286        TCGA-BR-8289 
"5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" 
       TCGA-BR-8291        TCGA-BR-8295        TCGA-BR-8296        TCGA-BR-8297 
"5P LOSS WILD-TYPE"       "5P LOSS CNV" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" 
       TCGA-BR-8592        TCGA-BR-A4IU        TCGA-BR-A4IV        TCGA-BR-A4IY 
"5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" 
       TCGA-BR-A4IZ        TCGA-BR-A4J1        TCGA-BR-A4J2        TCGA-BR-A4J4 
"5P LOSS WILD-TYPE"       "5P LOSS CNV" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" 
       TCGA-BR-A4J5        TCGA-BR-A4J6        TCGA-BR-A4J8        TCGA-BR-A4J9 
"5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" 
       TCGA-BR-A4PF        TCGA-BR-A4QI        TCGA-BR-A4QL        TCGA-CD-5798 
"5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" 
       TCGA-CD-5799        TCGA-CD-5800        TCGA-CD-5801        TCGA-CD-5802 
"5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" 
       TCGA-CD-5803        TCGA-CG-4300        TCGA-CG-4301        TCGA-CG-4304 
"5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" 
       TCGA-CG-4305        TCGA-CG-4306        TCGA-CG-4436        TCGA-CG-4437 
"5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" 
       TCGA-CG-4438        TCGA-CG-4440        TCGA-CG-4441        TCGA-CG-4443 
"5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" 
       TCGA-CG-4444        TCGA-CG-4449        TCGA-CG-4455        TCGA-CG-4460 
"5P LOSS WILD-TYPE"       "5P LOSS CNV" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" 
       TCGA-CG-4462        TCGA-CG-4465        TCGA-CG-4466        TCGA-CG-4469 
"5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" 
       TCGA-CG-4472        TCGA-CG-4474        TCGA-CG-4477        TCGA-CG-5716 
"5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" 
       TCGA-CG-5717        TCGA-CG-5718        TCGA-CG-5719        TCGA-CG-5720 
"5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" 
       TCGA-CG-5721        TCGA-CG-5722        TCGA-CG-5723        TCGA-CG-5724 
"5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" 
       TCGA-CG-5725        TCGA-CG-5726        TCGA-CG-5727        TCGA-CG-5728 
"5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" 
       TCGA-CG-5730        TCGA-CG-5732        TCGA-CG-5733        TCGA-CG-5734 
"5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" 
       TCGA-D7-5577        TCGA-D7-5578        TCGA-D7-5579        TCGA-D7-6518 
"5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" 
       TCGA-D7-6519        TCGA-D7-6520        TCGA-D7-6521        TCGA-D7-6522 
"5P LOSS WILD-TYPE"       "5P LOSS CNV" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" 
       TCGA-D7-6524        TCGA-D7-6525        TCGA-D7-6526        TCGA-D7-6527 
"5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" 
       TCGA-D7-6528        TCGA-D7-6815        TCGA-D7-6817        TCGA-D7-6818 
"5P LOSS WILD-TYPE"       "5P LOSS CNV" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" 
       TCGA-D7-6820        TCGA-D7-6822        TCGA-EQ-5647        TCGA-EQ-8122 
"5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" 
       TCGA-F1-6177        TCGA-F1-6874        TCGA-F1-6875        TCGA-FP-7735 
"5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" 
       TCGA-FP-7829        TCGA-FP-7916        TCGA-FP-7998        TCGA-FP-8099 
"5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" 
       TCGA-FP-8209        TCGA-FP-8210        TCGA-FP-8631        TCGA-HJ-7597 
"5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE"       "5P LOSS CNV" "5P LOSS WILD-TYPE" 
       TCGA-IN-7806        TCGA-IN-7808        TCGA-IP-7968 
      "5P LOSS CNV" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" 
       TCGA-B7-5816        TCGA-B7-5818        TCGA-BR-6452        TCGA-BR-6455 
"5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" 
       TCGA-BR-6457        TCGA-BR-6458        TCGA-BR-6563        TCGA-BR-6564 
"5P LOSS WILD-TYPE"       "5P LOSS CNV" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" 
       TCGA-BR-6565        TCGA-BR-6566        TCGA-BR-6705        TCGA-BR-6706 
"5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" 
       TCGA-BR-6707        TCGA-BR-6709        TCGA-BR-6710        TCGA-BR-6801 
"5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" 
       TCGA-BR-6802        TCGA-BR-6803        TCGA-BR-6852        TCGA-BR-7196 
"5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" 
       TCGA-BR-7197        TCGA-BR-7703        TCGA-BR-7704        TCGA-BR-7707 
"5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" 
       TCGA-BR-7715        TCGA-BR-7716        TCGA-BR-7717        TCGA-BR-7722 
"5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" 
       TCGA-BR-7723        TCGA-BR-7851        TCGA-BR-7901        TCGA-BR-7957 
"5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" 
       TCGA-BR-7958        TCGA-BR-7959        TCGA-BR-8059        TCGA-BR-8060 
"5P LOSS WILD-TYPE"       "5P LOSS CNV" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" 
       TCGA-BR-8077        TCGA-BR-8078        TCGA-BR-8080        TCGA-BR-8081 
"5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" 
       TCGA-BR-8284        TCGA-BR-8285        TCGA-BR-8286        TCGA-BR-8289 
"5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" 
       TCGA-BR-8291        TCGA-BR-8295        TCGA-BR-8296        TCGA-BR-8297 
"5P LOSS WILD-TYPE"       "5P LOSS CNV" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" 
       TCGA-BR-8592        TCGA-BR-A4IU        TCGA-BR-A4IV        TCGA-BR-A4IY 
"5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" 
       TCGA-BR-A4IZ        TCGA-BR-A4J1        TCGA-BR-A4J2        TCGA-BR-A4J4 
"5P LOSS WILD-TYPE"       "5P LOSS CNV" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" 
       TCGA-BR-A4J5        TCGA-BR-A4J6        TCGA-BR-A4J8        TCGA-BR-A4J9 
"5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" 
       TCGA-BR-A4PF        TCGA-BR-A4QI        TCGA-BR-A4QL        TCGA-CD-5798 
"5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" 
       TCGA-CD-5799        TCGA-CD-5800        TCGA-CD-5801        TCGA-CD-5802 
"5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" 
       TCGA-CD-5803        TCGA-CG-4300        TCGA-CG-4301        TCGA-CG-4304 
"5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" 
       TCGA-CG-4305        TCGA-CG-4306        TCGA-CG-4436        TCGA-CG-4437 
"5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" 
       TCGA-CG-4438        TCGA-CG-4440        TCGA-CG-4441        TCGA-CG-4443 
"5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" 
       TCGA-CG-4444        TCGA-CG-4449        TCGA-CG-4455        TCGA-CG-4460 
"5P LOSS WILD-TYPE"       "5P LOSS CNV" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" 
       TCGA-CG-4462        TCGA-CG-4465        TCGA-CG-4466        TCGA-CG-4469 
"5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" 
       TCGA-CG-4472        TCGA-CG-4474        TCGA-CG-4477        TCGA-CG-5716 
"5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" 
       TCGA-CG-5717        TCGA-CG-5718        TCGA-CG-5719        TCGA-CG-5720 
"5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" 
       TCGA-CG-5721        TCGA-CG-5722        TCGA-CG-5723        TCGA-CG-5724 
"5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" 
       TCGA-CG-5725        TCGA-CG-5726        TCGA-CG-5727        TCGA-CG-5728 
"5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" 
       TCGA-CG-5730        TCGA-CG-5732        TCGA-CG-5733        TCGA-CG-5734 
"5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" 
       TCGA-D7-5577        TCGA-D7-5578        TCGA-D7-5579        TCGA-D7-6518 
"5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" 
       TCGA-D7-6519        TCGA-D7-6520        TCGA-D7-6521        TCGA-D7-6522 
"5P LOSS WILD-TYPE"       "5P LOSS CNV" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" 
       TCGA-D7-6524        TCGA-D7-6525        TCGA-D7-6526        TCGA-D7-6527 
"5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" 
       TCGA-D7-6528        TCGA-D7-6815        TCGA-D7-6817        TCGA-D7-6818 
"5P LOSS WILD-TYPE"       "5P LOSS CNV" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" 
       TCGA-D7-6820        TCGA-D7-6822        TCGA-EQ-5647        TCGA-EQ-8122 
"5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" 
       TCGA-F1-6177        TCGA-F1-6874        TCGA-F1-6875        TCGA-FP-7735 
"5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" 
       TCGA-FP-7829        TCGA-FP-7916        TCGA-FP-7998        TCGA-FP-8099 
"5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" 
       TCGA-FP-8209        TCGA-FP-8210        TCGA-FP-8631        TCGA-HJ-7597 
"5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE"       "5P LOSS CNV" "5P LOSS WILD-TYPE" 
       TCGA-IN-7806        TCGA-IN-7808        TCGA-IP-7968 
      "5P LOSS CNV" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" 
       TCGA-B7-5816        TCGA-B7-5818        TCGA-BR-6452        TCGA-BR-6455 
"5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" 
       TCGA-BR-6457        TCGA-BR-6458        TCGA-BR-6563        TCGA-BR-6564 
"5P LOSS WILD-TYPE"       "5P LOSS CNV" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" 
       TCGA-BR-6565        TCGA-BR-6566        TCGA-BR-6705        TCGA-BR-6706 
"5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" 
       TCGA-BR-6707        TCGA-BR-6709        TCGA-BR-6710        TCGA-BR-6801 
"5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" 
       TCGA-BR-6802        TCGA-BR-6803        TCGA-BR-6852        TCGA-BR-7196 
"5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" 
       TCGA-BR-7197        TCGA-BR-7703        TCGA-BR-7704        TCGA-BR-7707 
"5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" 
       TCGA-BR-7715        TCGA-BR-7716        TCGA-BR-7717        TCGA-BR-7722 
"5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" 
       TCGA-BR-7723        TCGA-BR-7851        TCGA-BR-7901        TCGA-BR-7957 
"5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" 
       TCGA-BR-7958        TCGA-BR-7959        TCGA-BR-8059        TCGA-BR-8060 
"5P LOSS WILD-TYPE"       "5P LOSS CNV" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" 
       TCGA-BR-8077        TCGA-BR-8078        TCGA-BR-8080        TCGA-BR-8081 
"5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" 
       TCGA-BR-8284        TCGA-BR-8285        TCGA-BR-8286        TCGA-BR-8289 
"5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" 
       TCGA-BR-8291        TCGA-BR-8295        TCGA-BR-8296        TCGA-BR-8297 
"5P LOSS WILD-TYPE"       "5P LOSS CNV" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" 
       TCGA-BR-8592        TCGA-BR-A4IU        TCGA-BR-A4IV        TCGA-BR-A4IY 
"5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" 
       TCGA-BR-A4IZ        TCGA-BR-A4J1        TCGA-BR-A4J2        TCGA-BR-A4J4 
"5P LOSS WILD-TYPE"       "5P LOSS CNV" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" 
       TCGA-BR-A4J5        TCGA-BR-A4J6        TCGA-BR-A4J8        TCGA-BR-A4J9 
"5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" 
       TCGA-BR-A4PF        TCGA-BR-A4QI        TCGA-BR-A4QL        TCGA-CD-5798 
"5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" 
       TCGA-CD-5799        TCGA-CD-5800        TCGA-CD-5801        TCGA-CD-5802 
"5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" 
       TCGA-CD-5803        TCGA-CG-4300        TCGA-CG-4301        TCGA-CG-4304 
"5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" 
       TCGA-CG-4305        TCGA-CG-4306        TCGA-CG-4436        TCGA-CG-4437 
"5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" 
       TCGA-CG-4438        TCGA-CG-4440        TCGA-CG-4441        TCGA-CG-4443 
"5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" 
       TCGA-CG-4444        TCGA-CG-4449        TCGA-CG-4455        TCGA-CG-4460 
"5P LOSS WILD-TYPE"       "5P LOSS CNV" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" 
       TCGA-CG-4462        TCGA-CG-4465        TCGA-CG-4466        TCGA-CG-4469 
"5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" 
       TCGA-CG-4472        TCGA-CG-4474        TCGA-CG-4477        TCGA-CG-5716 
"5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" 
       TCGA-CG-5717        TCGA-CG-5718        TCGA-CG-5719        TCGA-CG-5720 
"5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" 
       TCGA-CG-5721        TCGA-CG-5722        TCGA-CG-5723        TCGA-CG-5724 
"5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" 
       TCGA-CG-5725        TCGA-CG-5726        TCGA-CG-5727        TCGA-CG-5728 
"5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" 
       TCGA-CG-5730        TCGA-CG-5732        TCGA-CG-5733        TCGA-CG-5734 
"5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" 
       TCGA-D7-5577        TCGA-D7-5578        TCGA-D7-5579        TCGA-D7-6518 
"5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" 
       TCGA-D7-6519        TCGA-D7-6520        TCGA-D7-6521        TCGA-D7-6522 
"5P LOSS WILD-TYPE"       "5P LOSS CNV" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" 
       TCGA-D7-6524        TCGA-D7-6525        TCGA-D7-6526        TCGA-D7-6527 
"5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" 
       TCGA-D7-6528        TCGA-D7-6815        TCGA-D7-6817        TCGA-D7-6818 
"5P LOSS WILD-TYPE"       "5P LOSS CNV" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" 
       TCGA-D7-6820        TCGA-D7-6822        TCGA-EQ-5647        TCGA-EQ-8122 
"5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" 
       TCGA-F1-6177        TCGA-F1-6874        TCGA-F1-6875        TCGA-FP-7735 
"5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" 
       TCGA-FP-7829        TCGA-FP-7916        TCGA-FP-7998        TCGA-FP-8099 
"5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" 
       TCGA-FP-8209        TCGA-FP-8210        TCGA-FP-8631        TCGA-HJ-7597 
"5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE"       "5P LOSS CNV" "5P LOSS WILD-TYPE" 
       TCGA-IN-7806        TCGA-IN-7808        TCGA-IP-7968 
      "5P LOSS CNV" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" 
[1] "hr=" "1.2"
D44V2, continuous
D44V3, binary
[1] "tbl2"
                   cls
clus                [,1] [,2]
  5P LOSS CNV          3    7
  5P LOSS WILD-TYPE   69  101
        clus
vv       5P LOSS CNV 5P LOSS WILD-TYPE
  FEMALE           3                69
  MALE             7               101
                   vv
clus                STOMACH  ADENOCARCINOMA  DIFFUSE TYPE
  5P LOSS CNV                                           0
  5P LOSS WILD-TYPE                                    10
                   vv
clus                STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  5P LOSS CNV                                                            2
  5P LOSS WILD-TYPE                                                     14
                   vv
clus                STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  5P LOSS CNV                                                                       1
  5P LOSS WILD-TYPE                                                                 7
                   vv
clus                STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE
  5P LOSS CNV                                                              1
  5P LOSS WILD-TYPE                                                        2
                   vv
clus                STOMACH ADENOCARCINOMA  SIGNET RING TYPE
  5P LOSS CNV                                              0
  5P LOSS WILD-TYPE                                        1
                   vv
clus                STOMACH ADENOCARCINOMA - DIFFUSE TYPE
  5P LOSS CNV                                           1
  5P LOSS WILD-TYPE                                    15
                   vv
clus                STOMACH ADENOCARCINOMA - NOT OTHERWISE SPECIFIED (NOS)
  5P LOSS CNV                                                            2
  5P LOSS WILD-TYPE                                                     71
                   vv
clus                STOMACH INTESTINAL ADENOCARCINOMA - MUCINOUS TYPE
  5P LOSS CNV                                                       1
  5P LOSS WILD-TYPE                                                 6
                   vv
clus                STOMACH INTESTINAL ADENOCARCINOMA - PAPILLARY TYPE
  5P LOSS CNV                                                        0
  5P LOSS WILD-TYPE                                                  3
                   vv
clus                STOMACH INTESTINAL ADENOCARCINOMA - TUBULAR TYPE
  5P LOSS CNV                                                      2
  5P LOSS WILD-TYPE                                                8
                   vv
clus                STOMACH INTESTINAL ADENOCARCINOMA - TYPE NOT OTHERWISE SPECIFIED (NOS)
  5P LOSS CNV                                                                            0
  5P LOSS WILD-TYPE                                                                     28
D44V4, multiclass
                   vv
clus                T1 T2 T3 T4
  5P LOSS CNV        0  3  2  0
  5P LOSS WILD-TYPE  6 49 54 18
D44V5, multiclass
    clus
vv   5P LOSS CNV 5P LOSS WILD-TYPE
  T1           0                 6
  T2           3                49
  T3           2                54
  T4           0                18
                   vv
clus                N0 N1 N2 N3
  5P LOSS CNV        0  4  2  0
  5P LOSS WILD-TYPE 44 45 21 15
D44V6, multiclass
    clus
vv   5P LOSS CNV 5P LOSS WILD-TYPE
  N0           0                44
  N1           4                45
  N2           2                21
  N3           0                15
                   vv
clus                 M0  M1  MX
  5P LOSS CNV         6   0   0
  5P LOSS WILD-TYPE 112  16   8
D44V7, multiclass
    clus
vv   5P LOSS CNV 5P LOSS WILD-TYPE
  M0           6               112
  M1           0                16
  MX           0                 8
                   vv
clus                 I II III IV
  5P LOSS CNV        0  2   3  0
  5P LOSS WILD-TYPE 24 35  36 26
D44V8, multiclass
     clus
vv    5P LOSS CNV 5P LOSS WILD-TYPE
  I             0                24
  II            2                35
  III           3                36
  IV            0                26
D44V9, binary
[1] "tbl2"
                   cls
clus                [,1] [,2]
  5P LOSS CNV          0   10
  5P LOSS WILD-TYPE    5  165
     clus
vv    5P LOSS CNV 5P LOSS WILD-TYPE
  NO            0                 5
  YES          10               165
                   vv
clus                 R0  R1  R2  RX
  5P LOSS CNV         9   0   0   1
  5P LOSS WILD-TYPE 116   7  12  24
D44V10, multiclass
    clus
vv   5P LOSS CNV 5P LOSS WILD-TYPE
  R0           9               116
  R1           0                 7
  R2           0                12
  RX           1                24
D44V11, continuous

Clustering(45) Variable = 5q loss
D45V1, survival
                   sevent
clus2                 0   1
  5Q LOSS CNV        17   2
  5Q LOSS WILD-TYPE 107  17
      5Q LOSS CNV 5Q LOSS WILD-TYPE 
               19               124 
      5Q LOSS CNV 5Q LOSS WILD-TYPE 
                2                17 
$`5Q LOSS CNV`
TCGA-BR-6458 TCGA-BR-7197 TCGA-BR-7901 TCGA-BR-7959 TCGA-BR-8286 TCGA-BR-8295 
        1.35         1.48         0.95         1.08         0.43         1.55 
TCGA-BR-A4J1 TCGA-BR-A4QI TCGA-CG-4304 TCGA-CG-4449 TCGA-CG-5718 TCGA-D7-6520 
        0.72         0.49        27.02        19.07         1.02         9.63 
TCGA-D7-6527 TCGA-D7-6815 TCGA-D7-6817 TCGA-D7-6822 TCGA-F1-6875 TCGA-FP-8631 
        4.14         3.65         4.70         4.27        72.23         0.56 
TCGA-IN-7806 
        6.87 

$`5Q LOSS WILD-TYPE`
TCGA-B7-5816 TCGA-B7-5818 TCGA-BR-6452 TCGA-BR-6455 TCGA-BR-6457 TCGA-BR-6563 
        5.62         0.10         0.95         1.41         1.35         0.85 
TCGA-BR-6564 TCGA-BR-6565 TCGA-BR-6566 TCGA-BR-6705 TCGA-BR-6706 TCGA-BR-6707 
        0.82         0.62         0.62         1.71         2.17         0.99 
TCGA-BR-6709 TCGA-BR-6710 TCGA-BR-6801 TCGA-BR-6802 TCGA-BR-6803 TCGA-BR-6852 
        1.22         0.66         1.12         0.76         0.66         0.26 
TCGA-BR-7196 TCGA-BR-7703 TCGA-BR-7704 TCGA-BR-7707 TCGA-BR-7715 TCGA-BR-7716 
        1.22         0.46         1.25         0.13         1.05         0.82 
TCGA-BR-7717 TCGA-BR-7722 TCGA-BR-7723 TCGA-BR-7851 TCGA-BR-7957 TCGA-BR-7958 
        0.69         0.16         4.54         0.99         0.69         0.16 
TCGA-BR-8059 TCGA-BR-8060 TCGA-BR-8077 TCGA-BR-8078 TCGA-BR-8080 TCGA-BR-8081 
        0.82         1.32         0.69         0.95         0.49         0.46 
TCGA-BR-8284 TCGA-BR-8285 TCGA-BR-8289 TCGA-BR-8291 TCGA-BR-8296 TCGA-BR-8297 
        0.72         0.26         0.26         1.18         1.48         0.76 
TCGA-BR-8592 TCGA-BR-A4IU TCGA-BR-A4IV TCGA-BR-A4IY TCGA-BR-A4IZ TCGA-BR-A4J2 
        0.20         0.59         0.92         0.39         0.79         0.79 
TCGA-BR-A4J4 TCGA-BR-A4J5 TCGA-BR-A4J6 TCGA-BR-A4J8 TCGA-BR-A4J9 TCGA-BR-A4PF 
        0.53         0.43         0.13         0.23         0.10         0.72 
TCGA-BR-A4QL TCGA-CD-5798 TCGA-CD-5799 TCGA-CD-5800 TCGA-CD-5801 TCGA-CD-5802 
        2.24         0.82         0.69         0.36         0.49         0.30 
TCGA-CD-5803 TCGA-CG-4300 TCGA-CG-4301 TCGA-CG-4305 TCGA-CG-4306 TCGA-CG-4436 
        0.07        20.02         3.02        15.95         1.02        52.96 
TCGA-CG-4437 TCGA-CG-4438 TCGA-CG-4440 TCGA-CG-4441 TCGA-CG-4443 TCGA-CG-4444 
        8.05        54.05         4.01        14.01        29.98        47.05 
TCGA-CG-4455 TCGA-CG-4460 TCGA-CG-4462 TCGA-CG-4465 TCGA-CG-4466 TCGA-CG-4469 
       12.03        21.99         1.02         8.98        18.94         7.07 
TCGA-CG-4472 TCGA-CG-4474 TCGA-CG-4477 TCGA-CG-5716 TCGA-CG-5717 TCGA-CG-5719 
       12.00         1.02         1.02         1.02         6.94         1.02 
TCGA-CG-5720 TCGA-CG-5721 TCGA-CG-5722 TCGA-CG-5723 TCGA-CG-5724 TCGA-CG-5725 
        0.99         5.98         0.95        70.06        12.03        15.02 
TCGA-CG-5726 TCGA-CG-5727 TCGA-CG-5728 TCGA-CG-5730 TCGA-CG-5732 TCGA-CG-5733 
       28.96        31.04        65.10         4.01        55.04        21.07 
TCGA-CG-5734 TCGA-D7-5577 TCGA-D7-5578 TCGA-D7-5579 TCGA-D7-6518 TCGA-D7-6519 
        7.99         8.65         3.58         4.54         9.80        15.65 
TCGA-D7-6521 TCGA-D7-6522 TCGA-D7-6524 TCGA-D7-6525 TCGA-D7-6526 TCGA-D7-6528 
        8.19         6.90         0.69         5.95         6.61         1.68 
TCGA-D7-6818 TCGA-D7-6820 TCGA-EQ-5647 TCGA-EQ-8122 TCGA-F1-6177 TCGA-F1-6874 
        4.04         2.93         0.62         7.79         6.54         2.01 
TCGA-FP-7735 TCGA-FP-7829 TCGA-FP-7916 TCGA-FP-7998 TCGA-FP-8099 TCGA-FP-8209 
        0.39         0.20         3.02         3.58         1.02        59.05 
TCGA-FP-8210 TCGA-HJ-7597 TCGA-IN-7808 TCGA-IP-7968 
        5.03        26.43         3.55         2.53 

      5Q LOSS CNV 5Q LOSS WILD-TYPE 
             0.43              0.07 
      5Q LOSS CNV 5Q LOSS WILD-TYPE 
            72.23             70.06 
      5Q LOSS CNV 5Q LOSS WILD-TYPE 
             1.55              1.20 
[1] "0.4 - 72.2 (1.6)" "0.1 - 70.1 (1.2)"
       TCGA-B7-5816        TCGA-B7-5818        TCGA-BR-6452        TCGA-BR-6455 
"5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" 
       TCGA-BR-6457        TCGA-BR-6458        TCGA-BR-6563        TCGA-BR-6564 
"5Q LOSS WILD-TYPE"       "5Q LOSS CNV" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" 
       TCGA-BR-6565        TCGA-BR-6566        TCGA-BR-6705        TCGA-BR-6706 
"5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" 
       TCGA-BR-6707        TCGA-BR-6709        TCGA-BR-6710        TCGA-BR-6801 
"5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" 
       TCGA-BR-6802        TCGA-BR-6803        TCGA-BR-6852        TCGA-BR-7196 
"5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" 
       TCGA-BR-7197        TCGA-BR-7703        TCGA-BR-7704        TCGA-BR-7707 
      "5Q LOSS CNV" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" 
       TCGA-BR-7715        TCGA-BR-7716        TCGA-BR-7717        TCGA-BR-7722 
"5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" 
       TCGA-BR-7723        TCGA-BR-7851        TCGA-BR-7901        TCGA-BR-7957 
"5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE"       "5Q LOSS CNV" "5Q LOSS WILD-TYPE" 
       TCGA-BR-7958        TCGA-BR-7959        TCGA-BR-8059        TCGA-BR-8060 
"5Q LOSS WILD-TYPE"       "5Q LOSS CNV" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" 
       TCGA-BR-8077        TCGA-BR-8078        TCGA-BR-8080        TCGA-BR-8081 
"5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" 
       TCGA-BR-8284        TCGA-BR-8285        TCGA-BR-8286        TCGA-BR-8289 
"5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE"       "5Q LOSS CNV" "5Q LOSS WILD-TYPE" 
       TCGA-BR-8291        TCGA-BR-8295        TCGA-BR-8296        TCGA-BR-8297 
"5Q LOSS WILD-TYPE"       "5Q LOSS CNV" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" 
       TCGA-BR-8592        TCGA-BR-A4IU        TCGA-BR-A4IV        TCGA-BR-A4IY 
"5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" 
       TCGA-BR-A4IZ        TCGA-BR-A4J1        TCGA-BR-A4J2        TCGA-BR-A4J4 
"5Q LOSS WILD-TYPE"       "5Q LOSS CNV" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" 
       TCGA-BR-A4J5        TCGA-BR-A4J6        TCGA-BR-A4J8        TCGA-BR-A4J9 
"5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" 
       TCGA-BR-A4PF        TCGA-BR-A4QI        TCGA-BR-A4QL        TCGA-CD-5798 
"5Q LOSS WILD-TYPE"       "5Q LOSS CNV" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" 
       TCGA-CD-5799        TCGA-CD-5800        TCGA-CD-5801        TCGA-CD-5802 
"5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" 
       TCGA-CD-5803        TCGA-CG-4300        TCGA-CG-4301        TCGA-CG-4304 
"5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE"       "5Q LOSS CNV" 
       TCGA-CG-4305        TCGA-CG-4306        TCGA-CG-4436        TCGA-CG-4437 
"5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" 
       TCGA-CG-4438        TCGA-CG-4440        TCGA-CG-4441        TCGA-CG-4443 
"5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" 
       TCGA-CG-4444        TCGA-CG-4449        TCGA-CG-4455        TCGA-CG-4460 
"5Q LOSS WILD-TYPE"       "5Q LOSS CNV" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" 
       TCGA-CG-4462        TCGA-CG-4465        TCGA-CG-4466        TCGA-CG-4469 
"5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" 
       TCGA-CG-4472        TCGA-CG-4474        TCGA-CG-4477        TCGA-CG-5716 
"5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" 
       TCGA-CG-5717        TCGA-CG-5718        TCGA-CG-5719        TCGA-CG-5720 
"5Q LOSS WILD-TYPE"       "5Q LOSS CNV" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" 
       TCGA-CG-5721        TCGA-CG-5722        TCGA-CG-5723        TCGA-CG-5724 
"5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" 
       TCGA-CG-5725        TCGA-CG-5726        TCGA-CG-5727        TCGA-CG-5728 
"5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" 
       TCGA-CG-5730        TCGA-CG-5732        TCGA-CG-5733        TCGA-CG-5734 
"5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" 
       TCGA-D7-5577        TCGA-D7-5578        TCGA-D7-5579        TCGA-D7-6518 
"5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" 
       TCGA-D7-6519        TCGA-D7-6520        TCGA-D7-6521        TCGA-D7-6522 
"5Q LOSS WILD-TYPE"       "5Q LOSS CNV" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" 
       TCGA-D7-6524        TCGA-D7-6525        TCGA-D7-6526        TCGA-D7-6527 
"5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE"       "5Q LOSS CNV" 
       TCGA-D7-6528        TCGA-D7-6815        TCGA-D7-6817        TCGA-D7-6818 
"5Q LOSS WILD-TYPE"       "5Q LOSS CNV"       "5Q LOSS CNV" "5Q LOSS WILD-TYPE" 
       TCGA-D7-6820        TCGA-D7-6822        TCGA-EQ-5647        TCGA-EQ-8122 
"5Q LOSS WILD-TYPE"       "5Q LOSS CNV" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" 
       TCGA-F1-6177        TCGA-F1-6874        TCGA-F1-6875        TCGA-FP-7735 
"5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE"       "5Q LOSS CNV" "5Q LOSS WILD-TYPE" 
       TCGA-FP-7829        TCGA-FP-7916        TCGA-FP-7998        TCGA-FP-8099 
"5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" 
       TCGA-FP-8209        TCGA-FP-8210        TCGA-FP-8631        TCGA-HJ-7597 
"5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE"       "5Q LOSS CNV" "5Q LOSS WILD-TYPE" 
       TCGA-IN-7806        TCGA-IN-7808        TCGA-IP-7968 
      "5Q LOSS CNV" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" 
       TCGA-B7-5816        TCGA-B7-5818        TCGA-BR-6452        TCGA-BR-6455 
"5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" 
       TCGA-BR-6457        TCGA-BR-6458        TCGA-BR-6563        TCGA-BR-6564 
"5Q LOSS WILD-TYPE"       "5Q LOSS CNV" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" 
       TCGA-BR-6565        TCGA-BR-6566        TCGA-BR-6705        TCGA-BR-6706 
"5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" 
       TCGA-BR-6707        TCGA-BR-6709        TCGA-BR-6710        TCGA-BR-6801 
"5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" 
       TCGA-BR-6802        TCGA-BR-6803        TCGA-BR-6852        TCGA-BR-7196 
"5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" 
       TCGA-BR-7197        TCGA-BR-7703        TCGA-BR-7704        TCGA-BR-7707 
      "5Q LOSS CNV" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" 
       TCGA-BR-7715        TCGA-BR-7716        TCGA-BR-7717        TCGA-BR-7722 
"5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" 
       TCGA-BR-7723        TCGA-BR-7851        TCGA-BR-7901        TCGA-BR-7957 
"5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE"       "5Q LOSS CNV" "5Q LOSS WILD-TYPE" 
       TCGA-BR-7958        TCGA-BR-7959        TCGA-BR-8059        TCGA-BR-8060 
"5Q LOSS WILD-TYPE"       "5Q LOSS CNV" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" 
       TCGA-BR-8077        TCGA-BR-8078        TCGA-BR-8080        TCGA-BR-8081 
"5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" 
       TCGA-BR-8284        TCGA-BR-8285        TCGA-BR-8286        TCGA-BR-8289 
"5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE"       "5Q LOSS CNV" "5Q LOSS WILD-TYPE" 
       TCGA-BR-8291        TCGA-BR-8295        TCGA-BR-8296        TCGA-BR-8297 
"5Q LOSS WILD-TYPE"       "5Q LOSS CNV" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" 
       TCGA-BR-8592        TCGA-BR-A4IU        TCGA-BR-A4IV        TCGA-BR-A4IY 
"5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" 
       TCGA-BR-A4IZ        TCGA-BR-A4J1        TCGA-BR-A4J2        TCGA-BR-A4J4 
"5Q LOSS WILD-TYPE"       "5Q LOSS CNV" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" 
       TCGA-BR-A4J5        TCGA-BR-A4J6        TCGA-BR-A4J8        TCGA-BR-A4J9 
"5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" 
       TCGA-BR-A4PF        TCGA-BR-A4QI        TCGA-BR-A4QL        TCGA-CD-5798 
"5Q LOSS WILD-TYPE"       "5Q LOSS CNV" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" 
       TCGA-CD-5799        TCGA-CD-5800        TCGA-CD-5801        TCGA-CD-5802 
"5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" 
       TCGA-CD-5803        TCGA-CG-4300        TCGA-CG-4301        TCGA-CG-4304 
"5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE"       "5Q LOSS CNV" 
       TCGA-CG-4305        TCGA-CG-4306        TCGA-CG-4436        TCGA-CG-4437 
"5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" 
       TCGA-CG-4438        TCGA-CG-4440        TCGA-CG-4441        TCGA-CG-4443 
"5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" 
       TCGA-CG-4444        TCGA-CG-4449        TCGA-CG-4455        TCGA-CG-4460 
"5Q LOSS WILD-TYPE"       "5Q LOSS CNV" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" 
       TCGA-CG-4462        TCGA-CG-4465        TCGA-CG-4466        TCGA-CG-4469 
"5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" 
       TCGA-CG-4472        TCGA-CG-4474        TCGA-CG-4477        TCGA-CG-5716 
"5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" 
       TCGA-CG-5717        TCGA-CG-5718        TCGA-CG-5719        TCGA-CG-5720 
"5Q LOSS WILD-TYPE"       "5Q LOSS CNV" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" 
       TCGA-CG-5721        TCGA-CG-5722        TCGA-CG-5723        TCGA-CG-5724 
"5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" 
       TCGA-CG-5725        TCGA-CG-5726        TCGA-CG-5727        TCGA-CG-5728 
"5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" 
       TCGA-CG-5730        TCGA-CG-5732        TCGA-CG-5733        TCGA-CG-5734 
"5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" 
       TCGA-D7-5577        TCGA-D7-5578        TCGA-D7-5579        TCGA-D7-6518 
"5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" 
       TCGA-D7-6519        TCGA-D7-6520        TCGA-D7-6521        TCGA-D7-6522 
"5Q LOSS WILD-TYPE"       "5Q LOSS CNV" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" 
       TCGA-D7-6524        TCGA-D7-6525        TCGA-D7-6526        TCGA-D7-6527 
"5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE"       "5Q LOSS CNV" 
       TCGA-D7-6528        TCGA-D7-6815        TCGA-D7-6817        TCGA-D7-6818 
"5Q LOSS WILD-TYPE"       "5Q LOSS CNV"       "5Q LOSS CNV" "5Q LOSS WILD-TYPE" 
       TCGA-D7-6820        TCGA-D7-6822        TCGA-EQ-5647        TCGA-EQ-8122 
"5Q LOSS WILD-TYPE"       "5Q LOSS CNV" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" 
       TCGA-F1-6177        TCGA-F1-6874        TCGA-F1-6875        TCGA-FP-7735 
"5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE"       "5Q LOSS CNV" "5Q LOSS WILD-TYPE" 
       TCGA-FP-7829        TCGA-FP-7916        TCGA-FP-7998        TCGA-FP-8099 
"5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" 
       TCGA-FP-8209        TCGA-FP-8210        TCGA-FP-8631        TCGA-HJ-7597 
"5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE"       "5Q LOSS CNV" "5Q LOSS WILD-TYPE" 
       TCGA-IN-7806        TCGA-IN-7808        TCGA-IP-7968 
      "5Q LOSS CNV" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" 
       TCGA-B7-5816        TCGA-B7-5818        TCGA-BR-6452        TCGA-BR-6455 
"5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" 
       TCGA-BR-6457        TCGA-BR-6458        TCGA-BR-6563        TCGA-BR-6564 
"5Q LOSS WILD-TYPE"       "5Q LOSS CNV" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" 
       TCGA-BR-6565        TCGA-BR-6566        TCGA-BR-6705        TCGA-BR-6706 
"5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" 
       TCGA-BR-6707        TCGA-BR-6709        TCGA-BR-6710        TCGA-BR-6801 
"5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" 
       TCGA-BR-6802        TCGA-BR-6803        TCGA-BR-6852        TCGA-BR-7196 
"5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" 
       TCGA-BR-7197        TCGA-BR-7703        TCGA-BR-7704        TCGA-BR-7707 
      "5Q LOSS CNV" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" 
       TCGA-BR-7715        TCGA-BR-7716        TCGA-BR-7717        TCGA-BR-7722 
"5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" 
       TCGA-BR-7723        TCGA-BR-7851        TCGA-BR-7901        TCGA-BR-7957 
"5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE"       "5Q LOSS CNV" "5Q LOSS WILD-TYPE" 
       TCGA-BR-7958        TCGA-BR-7959        TCGA-BR-8059        TCGA-BR-8060 
"5Q LOSS WILD-TYPE"       "5Q LOSS CNV" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" 
       TCGA-BR-8077        TCGA-BR-8078        TCGA-BR-8080        TCGA-BR-8081 
"5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" 
       TCGA-BR-8284        TCGA-BR-8285        TCGA-BR-8286        TCGA-BR-8289 
"5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE"       "5Q LOSS CNV" "5Q LOSS WILD-TYPE" 
       TCGA-BR-8291        TCGA-BR-8295        TCGA-BR-8296        TCGA-BR-8297 
"5Q LOSS WILD-TYPE"       "5Q LOSS CNV" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" 
       TCGA-BR-8592        TCGA-BR-A4IU        TCGA-BR-A4IV        TCGA-BR-A4IY 
"5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" 
       TCGA-BR-A4IZ        TCGA-BR-A4J1        TCGA-BR-A4J2        TCGA-BR-A4J4 
"5Q LOSS WILD-TYPE"       "5Q LOSS CNV" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" 
       TCGA-BR-A4J5        TCGA-BR-A4J6        TCGA-BR-A4J8        TCGA-BR-A4J9 
"5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" 
       TCGA-BR-A4PF        TCGA-BR-A4QI        TCGA-BR-A4QL        TCGA-CD-5798 
"5Q LOSS WILD-TYPE"       "5Q LOSS CNV" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" 
       TCGA-CD-5799        TCGA-CD-5800        TCGA-CD-5801        TCGA-CD-5802 
"5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" 
       TCGA-CD-5803        TCGA-CG-4300        TCGA-CG-4301        TCGA-CG-4304 
"5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE"       "5Q LOSS CNV" 
       TCGA-CG-4305        TCGA-CG-4306        TCGA-CG-4436        TCGA-CG-4437 
"5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" 
       TCGA-CG-4438        TCGA-CG-4440        TCGA-CG-4441        TCGA-CG-4443 
"5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" 
       TCGA-CG-4444        TCGA-CG-4449        TCGA-CG-4455        TCGA-CG-4460 
"5Q LOSS WILD-TYPE"       "5Q LOSS CNV" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" 
       TCGA-CG-4462        TCGA-CG-4465        TCGA-CG-4466        TCGA-CG-4469 
"5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" 
       TCGA-CG-4472        TCGA-CG-4474        TCGA-CG-4477        TCGA-CG-5716 
"5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" 
       TCGA-CG-5717        TCGA-CG-5718        TCGA-CG-5719        TCGA-CG-5720 
"5Q LOSS WILD-TYPE"       "5Q LOSS CNV" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" 
       TCGA-CG-5721        TCGA-CG-5722        TCGA-CG-5723        TCGA-CG-5724 
"5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" 
       TCGA-CG-5725        TCGA-CG-5726        TCGA-CG-5727        TCGA-CG-5728 
"5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" 
       TCGA-CG-5730        TCGA-CG-5732        TCGA-CG-5733        TCGA-CG-5734 
"5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" 
       TCGA-D7-5577        TCGA-D7-5578        TCGA-D7-5579        TCGA-D7-6518 
"5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" 
       TCGA-D7-6519        TCGA-D7-6520        TCGA-D7-6521        TCGA-D7-6522 
"5Q LOSS WILD-TYPE"       "5Q LOSS CNV" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" 
       TCGA-D7-6524        TCGA-D7-6525        TCGA-D7-6526        TCGA-D7-6527 
"5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE"       "5Q LOSS CNV" 
       TCGA-D7-6528        TCGA-D7-6815        TCGA-D7-6817        TCGA-D7-6818 
"5Q LOSS WILD-TYPE"       "5Q LOSS CNV"       "5Q LOSS CNV" "5Q LOSS WILD-TYPE" 
       TCGA-D7-6820        TCGA-D7-6822        TCGA-EQ-5647        TCGA-EQ-8122 
"5Q LOSS WILD-TYPE"       "5Q LOSS CNV" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" 
       TCGA-F1-6177        TCGA-F1-6874        TCGA-F1-6875        TCGA-FP-7735 
"5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE"       "5Q LOSS CNV" "5Q LOSS WILD-TYPE" 
       TCGA-FP-7829        TCGA-FP-7916        TCGA-FP-7998        TCGA-FP-8099 
"5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" 
       TCGA-FP-8209        TCGA-FP-8210        TCGA-FP-8631        TCGA-HJ-7597 
"5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE"       "5Q LOSS CNV" "5Q LOSS WILD-TYPE" 
       TCGA-IN-7806        TCGA-IN-7808        TCGA-IP-7968 
      "5Q LOSS CNV" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" 
[1] "hr=" "2.8"
D45V2, continuous
D45V3, binary
[1] "tbl2"
                   cls
clus                [,1] [,2]
  5Q LOSS CNV          5   15
  5Q LOSS WILD-TYPE   67   93
        clus
vv       5Q LOSS CNV 5Q LOSS WILD-TYPE
  FEMALE           5                67
  MALE            15                93
                   vv
clus                STOMACH  ADENOCARCINOMA  DIFFUSE TYPE
  5Q LOSS CNV                                           0
  5Q LOSS WILD-TYPE                                    10
                   vv
clus                STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  5Q LOSS CNV                                                            4
  5Q LOSS WILD-TYPE                                                     12
                   vv
clus                STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  5Q LOSS CNV                                                                       1
  5Q LOSS WILD-TYPE                                                                 7
                   vv
clus                STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE
  5Q LOSS CNV                                                              1
  5Q LOSS WILD-TYPE                                                        2
                   vv
clus                STOMACH ADENOCARCINOMA  SIGNET RING TYPE
  5Q LOSS CNV                                              0
  5Q LOSS WILD-TYPE                                        1
                   vv
clus                STOMACH ADENOCARCINOMA - DIFFUSE TYPE
  5Q LOSS CNV                                           1
  5Q LOSS WILD-TYPE                                    15
                   vv
clus                STOMACH ADENOCARCINOMA - NOT OTHERWISE SPECIFIED (NOS)
  5Q LOSS CNV                                                            6
  5Q LOSS WILD-TYPE                                                     67
                   vv
clus                STOMACH INTESTINAL ADENOCARCINOMA - MUCINOUS TYPE
  5Q LOSS CNV                                                       1
  5Q LOSS WILD-TYPE                                                 6
                   vv
clus                STOMACH INTESTINAL ADENOCARCINOMA - PAPILLARY TYPE
  5Q LOSS CNV                                                        1
  5Q LOSS WILD-TYPE                                                  2
                   vv
clus                STOMACH INTESTINAL ADENOCARCINOMA - TUBULAR TYPE
  5Q LOSS CNV                                                      4
  5Q LOSS WILD-TYPE                                                6
                   vv
clus                STOMACH INTESTINAL ADENOCARCINOMA - TYPE NOT OTHERWISE SPECIFIED (NOS)
  5Q LOSS CNV                                                                            1
  5Q LOSS WILD-TYPE                                                                     27
D45V4, multiclass
                   vv
clus                T1 T2 T3 T4
  5Q LOSS CNV        0  9  4  0
  5Q LOSS WILD-TYPE  6 43 52 18
D45V5, multiclass
    clus
vv   5Q LOSS CNV 5Q LOSS WILD-TYPE
  T1           0                 6
  T2           9                43
  T3           4                52
  T4           0                18
                   vv
clus                N0 N1 N2 N3
  5Q LOSS CNV        4  7  2  1
  5Q LOSS WILD-TYPE 40 42 21 14
D45V6, multiclass
    clus
vv   5Q LOSS CNV 5Q LOSS WILD-TYPE
  N0           4                40
  N1           7                42
  N2           2                21
  N3           1                14
                   vv
clus                 M0  M1  MX
  5Q LOSS CNV        14   0   0
  5Q LOSS WILD-TYPE 104  16   8
D45V7, multiclass
    clus
vv   5Q LOSS CNV 5Q LOSS WILD-TYPE
  M0          14               104
  M1           0                16
  MX           0                 8
                   vv
clus                 I II III IV
  5Q LOSS CNV        3  5   5  0
  5Q LOSS WILD-TYPE 21 32  34 26
D45V8, multiclass
     clus
vv    5Q LOSS CNV 5Q LOSS WILD-TYPE
  I             3                21
  II            5                32
  III           5                34
  IV            0                26
D45V9, binary
[1] "tbl2"
                   cls
clus                [,1] [,2]
  5Q LOSS CNV          1   19
  5Q LOSS WILD-TYPE    4  156
     clus
vv    5Q LOSS CNV 5Q LOSS WILD-TYPE
  NO            1                 4
  YES          19               156
                   vv
clus                 R0  R1  R2  RX
  5Q LOSS CNV        19   0   0   1
  5Q LOSS WILD-TYPE 106   7  12  24
D45V10, multiclass
    clus
vv   5Q LOSS CNV 5Q LOSS WILD-TYPE
  R0          19               106
  R1           0                 7
  R2           0                12
  RX           1                24
D45V11, continuous

Clustering(46) Variable = 6p loss
D46V1, survival
                   sevent
clus2                 0   1
  6P LOSS CNV         6   1
  6P LOSS WILD-TYPE 118  18
      6P LOSS CNV 6P LOSS WILD-TYPE 
                7               136 
      6P LOSS CNV 6P LOSS WILD-TYPE 
                1                18 
$`6P LOSS CNV`
TCGA-BR-A4J8 TCGA-BR-A4PF TCGA-CG-5719 TCGA-CG-5725 TCGA-D7-6520 TCGA-D7-6525 
        0.23         0.72         1.02        15.02         9.63         5.95 
TCGA-D7-6815 
        3.65 

$`6P LOSS WILD-TYPE`
TCGA-B7-5816 TCGA-B7-5818 TCGA-BR-6452 TCGA-BR-6455 TCGA-BR-6457 TCGA-BR-6458 
        5.62         0.10         0.95         1.41         1.35         1.35 
TCGA-BR-6563 TCGA-BR-6564 TCGA-BR-6565 TCGA-BR-6566 TCGA-BR-6705 TCGA-BR-6706 
        0.85         0.82         0.62         0.62         1.71         2.17 
TCGA-BR-6707 TCGA-BR-6709 TCGA-BR-6710 TCGA-BR-6801 TCGA-BR-6802 TCGA-BR-6803 
        0.99         1.22         0.66         1.12         0.76         0.66 
TCGA-BR-6852 TCGA-BR-7196 TCGA-BR-7197 TCGA-BR-7703 TCGA-BR-7704 TCGA-BR-7707 
        0.26         1.22         1.48         0.46         1.25         0.13 
TCGA-BR-7715 TCGA-BR-7716 TCGA-BR-7717 TCGA-BR-7722 TCGA-BR-7723 TCGA-BR-7851 
        1.05         0.82         0.69         0.16         4.54         0.99 
TCGA-BR-7901 TCGA-BR-7957 TCGA-BR-7958 TCGA-BR-7959 TCGA-BR-8059 TCGA-BR-8060 
        0.95         0.69         0.16         1.08         0.82         1.32 
TCGA-BR-8077 TCGA-BR-8078 TCGA-BR-8080 TCGA-BR-8081 TCGA-BR-8284 TCGA-BR-8285 
        0.69         0.95         0.49         0.46         0.72         0.26 
TCGA-BR-8286 TCGA-BR-8289 TCGA-BR-8291 TCGA-BR-8295 TCGA-BR-8296 TCGA-BR-8297 
        0.43         0.26         1.18         1.55         1.48         0.76 
TCGA-BR-8592 TCGA-BR-A4IU TCGA-BR-A4IV TCGA-BR-A4IY TCGA-BR-A4IZ TCGA-BR-A4J1 
        0.20         0.59         0.92         0.39         0.79         0.72 
TCGA-BR-A4J2 TCGA-BR-A4J4 TCGA-BR-A4J5 TCGA-BR-A4J6 TCGA-BR-A4J9 TCGA-BR-A4QI 
        0.79         0.53         0.43         0.13         0.10         0.49 
TCGA-BR-A4QL TCGA-CD-5798 TCGA-CD-5799 TCGA-CD-5800 TCGA-CD-5801 TCGA-CD-5802 
        2.24         0.82         0.69         0.36         0.49         0.30 
TCGA-CD-5803 TCGA-CG-4300 TCGA-CG-4301 TCGA-CG-4304 TCGA-CG-4305 TCGA-CG-4306 
        0.07        20.02         3.02        27.02        15.95         1.02 
TCGA-CG-4436 TCGA-CG-4437 TCGA-CG-4438 TCGA-CG-4440 TCGA-CG-4441 TCGA-CG-4443 
       52.96         8.05        54.05         4.01        14.01        29.98 
TCGA-CG-4444 TCGA-CG-4449 TCGA-CG-4455 TCGA-CG-4460 TCGA-CG-4462 TCGA-CG-4465 
       47.05        19.07        12.03        21.99         1.02         8.98 
TCGA-CG-4466 TCGA-CG-4469 TCGA-CG-4472 TCGA-CG-4474 TCGA-CG-4477 TCGA-CG-5716 
       18.94         7.07        12.00         1.02         1.02         1.02 
TCGA-CG-5717 TCGA-CG-5718 TCGA-CG-5720 TCGA-CG-5721 TCGA-CG-5722 TCGA-CG-5723 
        6.94         1.02         0.99         5.98         0.95        70.06 
TCGA-CG-5724 TCGA-CG-5726 TCGA-CG-5727 TCGA-CG-5728 TCGA-CG-5730 TCGA-CG-5732 
       12.03        28.96        31.04        65.10         4.01        55.04 
TCGA-CG-5733 TCGA-CG-5734 TCGA-D7-5577 TCGA-D7-5578 TCGA-D7-5579 TCGA-D7-6518 
       21.07         7.99         8.65         3.58         4.54         9.80 
TCGA-D7-6519 TCGA-D7-6521 TCGA-D7-6522 TCGA-D7-6524 TCGA-D7-6526 TCGA-D7-6527 
       15.65         8.19         6.90         0.69         6.61         4.14 
TCGA-D7-6528 TCGA-D7-6817 TCGA-D7-6818 TCGA-D7-6820 TCGA-D7-6822 TCGA-EQ-5647 
        1.68         4.70         4.04         2.93         4.27         0.62 
TCGA-EQ-8122 TCGA-F1-6177 TCGA-F1-6874 TCGA-F1-6875 TCGA-FP-7735 TCGA-FP-7829 
        7.79         6.54         2.01        72.23         0.39         0.20 
TCGA-FP-7916 TCGA-FP-7998 TCGA-FP-8099 TCGA-FP-8209 TCGA-FP-8210 TCGA-FP-8631 
        3.02         3.58         1.02        59.05         5.03         0.56 
TCGA-HJ-7597 TCGA-IN-7806 TCGA-IN-7808 TCGA-IP-7968 
       26.43         6.87         3.55         2.53 

      6P LOSS CNV 6P LOSS WILD-TYPE 
             0.23              0.07 
      6P LOSS CNV 6P LOSS WILD-TYPE 
            15.02             72.23 
      6P LOSS CNV 6P LOSS WILD-TYPE 
            3.650             1.235 
[1] "0.2 - 15.0 (3.6)" "0.1 - 72.2 (1.2)"
       TCGA-B7-5816        TCGA-B7-5818        TCGA-BR-6452        TCGA-BR-6455 
"6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" 
       TCGA-BR-6457        TCGA-BR-6458        TCGA-BR-6563        TCGA-BR-6564 
"6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" 
       TCGA-BR-6565        TCGA-BR-6566        TCGA-BR-6705        TCGA-BR-6706 
"6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" 
       TCGA-BR-6707        TCGA-BR-6709        TCGA-BR-6710        TCGA-BR-6801 
"6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" 
       TCGA-BR-6802        TCGA-BR-6803        TCGA-BR-6852        TCGA-BR-7196 
"6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" 
       TCGA-BR-7197        TCGA-BR-7703        TCGA-BR-7704        TCGA-BR-7707 
"6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" 
       TCGA-BR-7715        TCGA-BR-7716        TCGA-BR-7717        TCGA-BR-7722 
"6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" 
       TCGA-BR-7723        TCGA-BR-7851        TCGA-BR-7901        TCGA-BR-7957 
"6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" 
       TCGA-BR-7958        TCGA-BR-7959        TCGA-BR-8059        TCGA-BR-8060 
"6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" 
       TCGA-BR-8077        TCGA-BR-8078        TCGA-BR-8080        TCGA-BR-8081 
"6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" 
       TCGA-BR-8284        TCGA-BR-8285        TCGA-BR-8286        TCGA-BR-8289 
"6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" 
       TCGA-BR-8291        TCGA-BR-8295        TCGA-BR-8296        TCGA-BR-8297 
"6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" 
       TCGA-BR-8592        TCGA-BR-A4IU        TCGA-BR-A4IV        TCGA-BR-A4IY 
"6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" 
       TCGA-BR-A4IZ        TCGA-BR-A4J1        TCGA-BR-A4J2        TCGA-BR-A4J4 
"6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" 
       TCGA-BR-A4J5        TCGA-BR-A4J6        TCGA-BR-A4J8        TCGA-BR-A4J9 
"6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE"       "6P LOSS CNV" "6P LOSS WILD-TYPE" 
       TCGA-BR-A4PF        TCGA-BR-A4QI        TCGA-BR-A4QL        TCGA-CD-5798 
      "6P LOSS CNV" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" 
       TCGA-CD-5799        TCGA-CD-5800        TCGA-CD-5801        TCGA-CD-5802 
"6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" 
       TCGA-CD-5803        TCGA-CG-4300        TCGA-CG-4301        TCGA-CG-4304 
"6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" 
       TCGA-CG-4305        TCGA-CG-4306        TCGA-CG-4436        TCGA-CG-4437 
"6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" 
       TCGA-CG-4438        TCGA-CG-4440        TCGA-CG-4441        TCGA-CG-4443 
"6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" 
       TCGA-CG-4444        TCGA-CG-4449        TCGA-CG-4455        TCGA-CG-4460 
"6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" 
       TCGA-CG-4462        TCGA-CG-4465        TCGA-CG-4466        TCGA-CG-4469 
"6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" 
       TCGA-CG-4472        TCGA-CG-4474        TCGA-CG-4477        TCGA-CG-5716 
"6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" 
       TCGA-CG-5717        TCGA-CG-5718        TCGA-CG-5719        TCGA-CG-5720 
"6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE"       "6P LOSS CNV" "6P LOSS WILD-TYPE" 
       TCGA-CG-5721        TCGA-CG-5722        TCGA-CG-5723        TCGA-CG-5724 
"6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" 
       TCGA-CG-5725        TCGA-CG-5726        TCGA-CG-5727        TCGA-CG-5728 
      "6P LOSS CNV" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" 
       TCGA-CG-5730        TCGA-CG-5732        TCGA-CG-5733        TCGA-CG-5734 
"6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" 
       TCGA-D7-5577        TCGA-D7-5578        TCGA-D7-5579        TCGA-D7-6518 
"6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" 
       TCGA-D7-6519        TCGA-D7-6520        TCGA-D7-6521        TCGA-D7-6522 
"6P LOSS WILD-TYPE"       "6P LOSS CNV" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" 
       TCGA-D7-6524        TCGA-D7-6525        TCGA-D7-6526        TCGA-D7-6527 
"6P LOSS WILD-TYPE"       "6P LOSS CNV" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" 
       TCGA-D7-6528        TCGA-D7-6815        TCGA-D7-6817        TCGA-D7-6818 
"6P LOSS WILD-TYPE"       "6P LOSS CNV" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" 
       TCGA-D7-6820        TCGA-D7-6822        TCGA-EQ-5647        TCGA-EQ-8122 
"6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" 
       TCGA-F1-6177        TCGA-F1-6874        TCGA-F1-6875        TCGA-FP-7735 
"6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" 
       TCGA-FP-7829        TCGA-FP-7916        TCGA-FP-7998        TCGA-FP-8099 
"6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" 
       TCGA-FP-8209        TCGA-FP-8210        TCGA-FP-8631        TCGA-HJ-7597 
"6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" 
       TCGA-IN-7806        TCGA-IN-7808        TCGA-IP-7968 
"6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" 
       TCGA-B7-5816        TCGA-B7-5818        TCGA-BR-6452        TCGA-BR-6455 
"6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" 
       TCGA-BR-6457        TCGA-BR-6458        TCGA-BR-6563        TCGA-BR-6564 
"6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" 
       TCGA-BR-6565        TCGA-BR-6566        TCGA-BR-6705        TCGA-BR-6706 
"6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" 
       TCGA-BR-6707        TCGA-BR-6709        TCGA-BR-6710        TCGA-BR-6801 
"6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" 
       TCGA-BR-6802        TCGA-BR-6803        TCGA-BR-6852        TCGA-BR-7196 
"6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" 
       TCGA-BR-7197        TCGA-BR-7703        TCGA-BR-7704        TCGA-BR-7707 
"6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" 
       TCGA-BR-7715        TCGA-BR-7716        TCGA-BR-7717        TCGA-BR-7722 
"6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" 
       TCGA-BR-7723        TCGA-BR-7851        TCGA-BR-7901        TCGA-BR-7957 
"6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" 
       TCGA-BR-7958        TCGA-BR-7959        TCGA-BR-8059        TCGA-BR-8060 
"6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" 
       TCGA-BR-8077        TCGA-BR-8078        TCGA-BR-8080        TCGA-BR-8081 
"6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" 
       TCGA-BR-8284        TCGA-BR-8285        TCGA-BR-8286        TCGA-BR-8289 
"6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" 
       TCGA-BR-8291        TCGA-BR-8295        TCGA-BR-8296        TCGA-BR-8297 
"6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" 
       TCGA-BR-8592        TCGA-BR-A4IU        TCGA-BR-A4IV        TCGA-BR-A4IY 
"6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" 
       TCGA-BR-A4IZ        TCGA-BR-A4J1        TCGA-BR-A4J2        TCGA-BR-A4J4 
"6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" 
       TCGA-BR-A4J5        TCGA-BR-A4J6        TCGA-BR-A4J8        TCGA-BR-A4J9 
"6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE"       "6P LOSS CNV" "6P LOSS WILD-TYPE" 
       TCGA-BR-A4PF        TCGA-BR-A4QI        TCGA-BR-A4QL        TCGA-CD-5798 
      "6P LOSS CNV" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" 
       TCGA-CD-5799        TCGA-CD-5800        TCGA-CD-5801        TCGA-CD-5802 
"6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" 
       TCGA-CD-5803        TCGA-CG-4300        TCGA-CG-4301        TCGA-CG-4304 
"6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" 
       TCGA-CG-4305        TCGA-CG-4306        TCGA-CG-4436        TCGA-CG-4437 
"6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" 
       TCGA-CG-4438        TCGA-CG-4440        TCGA-CG-4441        TCGA-CG-4443 
"6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" 
       TCGA-CG-4444        TCGA-CG-4449        TCGA-CG-4455        TCGA-CG-4460 
"6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" 
       TCGA-CG-4462        TCGA-CG-4465        TCGA-CG-4466        TCGA-CG-4469 
"6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" 
       TCGA-CG-4472        TCGA-CG-4474        TCGA-CG-4477        TCGA-CG-5716 
"6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" 
       TCGA-CG-5717        TCGA-CG-5718        TCGA-CG-5719        TCGA-CG-5720 
"6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE"       "6P LOSS CNV" "6P LOSS WILD-TYPE" 
       TCGA-CG-5721        TCGA-CG-5722        TCGA-CG-5723        TCGA-CG-5724 
"6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" 
       TCGA-CG-5725        TCGA-CG-5726        TCGA-CG-5727        TCGA-CG-5728 
      "6P LOSS CNV" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" 
       TCGA-CG-5730        TCGA-CG-5732        TCGA-CG-5733        TCGA-CG-5734 
"6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" 
       TCGA-D7-5577        TCGA-D7-5578        TCGA-D7-5579        TCGA-D7-6518 
"6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" 
       TCGA-D7-6519        TCGA-D7-6520        TCGA-D7-6521        TCGA-D7-6522 
"6P LOSS WILD-TYPE"       "6P LOSS CNV" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" 
       TCGA-D7-6524        TCGA-D7-6525        TCGA-D7-6526        TCGA-D7-6527 
"6P LOSS WILD-TYPE"       "6P LOSS CNV" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" 
       TCGA-D7-6528        TCGA-D7-6815        TCGA-D7-6817        TCGA-D7-6818 
"6P LOSS WILD-TYPE"       "6P LOSS CNV" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" 
       TCGA-D7-6820        TCGA-D7-6822        TCGA-EQ-5647        TCGA-EQ-8122 
"6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" 
       TCGA-F1-6177        TCGA-F1-6874        TCGA-F1-6875        TCGA-FP-7735 
"6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" 
       TCGA-FP-7829        TCGA-FP-7916        TCGA-FP-7998        TCGA-FP-8099 
"6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" 
       TCGA-FP-8209        TCGA-FP-8210        TCGA-FP-8631        TCGA-HJ-7597 
"6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" 
       TCGA-IN-7806        TCGA-IN-7808        TCGA-IP-7968 
"6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" 
       TCGA-B7-5816        TCGA-B7-5818        TCGA-BR-6452        TCGA-BR-6455 
"6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" 
       TCGA-BR-6457        TCGA-BR-6458        TCGA-BR-6563        TCGA-BR-6564 
"6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" 
       TCGA-BR-6565        TCGA-BR-6566        TCGA-BR-6705        TCGA-BR-6706 
"6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" 
       TCGA-BR-6707        TCGA-BR-6709        TCGA-BR-6710        TCGA-BR-6801 
"6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" 
       TCGA-BR-6802        TCGA-BR-6803        TCGA-BR-6852        TCGA-BR-7196 
"6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" 
       TCGA-BR-7197        TCGA-BR-7703        TCGA-BR-7704        TCGA-BR-7707 
"6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" 
       TCGA-BR-7715        TCGA-BR-7716        TCGA-BR-7717        TCGA-BR-7722 
"6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" 
       TCGA-BR-7723        TCGA-BR-7851        TCGA-BR-7901        TCGA-BR-7957 
"6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" 
       TCGA-BR-7958        TCGA-BR-7959        TCGA-BR-8059        TCGA-BR-8060 
"6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" 
       TCGA-BR-8077        TCGA-BR-8078        TCGA-BR-8080        TCGA-BR-8081 
"6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" 
       TCGA-BR-8284        TCGA-BR-8285        TCGA-BR-8286        TCGA-BR-8289 
"6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" 
       TCGA-BR-8291        TCGA-BR-8295        TCGA-BR-8296        TCGA-BR-8297 
"6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" 
       TCGA-BR-8592        TCGA-BR-A4IU        TCGA-BR-A4IV        TCGA-BR-A4IY 
"6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" 
       TCGA-BR-A4IZ        TCGA-BR-A4J1        TCGA-BR-A4J2        TCGA-BR-A4J4 
"6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" 
       TCGA-BR-A4J5        TCGA-BR-A4J6        TCGA-BR-A4J8        TCGA-BR-A4J9 
"6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE"       "6P LOSS CNV" "6P LOSS WILD-TYPE" 
       TCGA-BR-A4PF        TCGA-BR-A4QI        TCGA-BR-A4QL        TCGA-CD-5798 
      "6P LOSS CNV" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" 
       TCGA-CD-5799        TCGA-CD-5800        TCGA-CD-5801        TCGA-CD-5802 
"6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" 
       TCGA-CD-5803        TCGA-CG-4300        TCGA-CG-4301        TCGA-CG-4304 
"6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" 
       TCGA-CG-4305        TCGA-CG-4306        TCGA-CG-4436        TCGA-CG-4437 
"6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" 
       TCGA-CG-4438        TCGA-CG-4440        TCGA-CG-4441        TCGA-CG-4443 
"6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" 
       TCGA-CG-4444        TCGA-CG-4449        TCGA-CG-4455        TCGA-CG-4460 
"6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" 
       TCGA-CG-4462        TCGA-CG-4465        TCGA-CG-4466        TCGA-CG-4469 
"6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" 
       TCGA-CG-4472        TCGA-CG-4474        TCGA-CG-4477        TCGA-CG-5716 
"6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" 
       TCGA-CG-5717        TCGA-CG-5718        TCGA-CG-5719        TCGA-CG-5720 
"6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE"       "6P LOSS CNV" "6P LOSS WILD-TYPE" 
       TCGA-CG-5721        TCGA-CG-5722        TCGA-CG-5723        TCGA-CG-5724 
"6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" 
       TCGA-CG-5725        TCGA-CG-5726        TCGA-CG-5727        TCGA-CG-5728 
      "6P LOSS CNV" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" 
       TCGA-CG-5730        TCGA-CG-5732        TCGA-CG-5733        TCGA-CG-5734 
"6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" 
       TCGA-D7-5577        TCGA-D7-5578        TCGA-D7-5579        TCGA-D7-6518 
"6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" 
       TCGA-D7-6519        TCGA-D7-6520        TCGA-D7-6521        TCGA-D7-6522 
"6P LOSS WILD-TYPE"       "6P LOSS CNV" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" 
       TCGA-D7-6524        TCGA-D7-6525        TCGA-D7-6526        TCGA-D7-6527 
"6P LOSS WILD-TYPE"       "6P LOSS CNV" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" 
       TCGA-D7-6528        TCGA-D7-6815        TCGA-D7-6817        TCGA-D7-6818 
"6P LOSS WILD-TYPE"       "6P LOSS CNV" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" 
       TCGA-D7-6820        TCGA-D7-6822        TCGA-EQ-5647        TCGA-EQ-8122 
"6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" 
       TCGA-F1-6177        TCGA-F1-6874        TCGA-F1-6875        TCGA-FP-7735 
"6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" 
       TCGA-FP-7829        TCGA-FP-7916        TCGA-FP-7998        TCGA-FP-8099 
"6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" 
       TCGA-FP-8209        TCGA-FP-8210        TCGA-FP-8631        TCGA-HJ-7597 
"6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" 
       TCGA-IN-7806        TCGA-IN-7808        TCGA-IP-7968 
"6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" 
[1] "hr=" "1.4"
D46V2, continuous
D46V3, binary
[1] "tbl2"
                   cls
clus                [,1] [,2]
  6P LOSS CNV          4    5
  6P LOSS WILD-TYPE   68  103
        clus
vv       6P LOSS CNV 6P LOSS WILD-TYPE
  FEMALE           4                68
  MALE             5               103
                   vv
clus                STOMACH  ADENOCARCINOMA  DIFFUSE TYPE
  6P LOSS CNV                                           0
  6P LOSS WILD-TYPE                                    10
                   vv
clus                STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  6P LOSS CNV                                                            2
  6P LOSS WILD-TYPE                                                     14
                   vv
clus                STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  6P LOSS CNV                                                                       0
  6P LOSS WILD-TYPE                                                                 8
                   vv
clus                STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE
  6P LOSS CNV                                                              0
  6P LOSS WILD-TYPE                                                        3
                   vv
clus                STOMACH ADENOCARCINOMA  SIGNET RING TYPE
  6P LOSS CNV                                              0
  6P LOSS WILD-TYPE                                        1
                   vv
clus                STOMACH ADENOCARCINOMA - DIFFUSE TYPE
  6P LOSS CNV                                           1
  6P LOSS WILD-TYPE                                    15
                   vv
clus                STOMACH ADENOCARCINOMA - NOT OTHERWISE SPECIFIED (NOS)
  6P LOSS CNV                                                            2
  6P LOSS WILD-TYPE                                                     71
                   vv
clus                STOMACH INTESTINAL ADENOCARCINOMA - MUCINOUS TYPE
  6P LOSS CNV                                                       0
  6P LOSS WILD-TYPE                                                 7
                   vv
clus                STOMACH INTESTINAL ADENOCARCINOMA - PAPILLARY TYPE
  6P LOSS CNV                                                        0
  6P LOSS WILD-TYPE                                                  3
                   vv
clus                STOMACH INTESTINAL ADENOCARCINOMA - TUBULAR TYPE
  6P LOSS CNV                                                      3
  6P LOSS WILD-TYPE                                                7
                   vv
clus                STOMACH INTESTINAL ADENOCARCINOMA - TYPE NOT OTHERWISE SPECIFIED (NOS)
  6P LOSS CNV                                                                            1
  6P LOSS WILD-TYPE                                                                     27
D46V4, multiclass
                   vv
clus                T1 T2 T3 T4
  6P LOSS CNV        0  5  1  1
  6P LOSS WILD-TYPE  6 47 55 17
D46V5, multiclass
    clus
vv   6P LOSS CNV 6P LOSS WILD-TYPE
  T1           0                 6
  T2           5                47
  T3           1                55
  T4           1                17
                   vv
clus                N0 N1 N2 N3
  6P LOSS CNV        2  0  3  0
  6P LOSS WILD-TYPE 42 49 20 15
D46V6, multiclass
    clus
vv   6P LOSS CNV 6P LOSS WILD-TYPE
  N0           2                42
  N1           0                49
  N2           3                20
  N3           0                15
                   vv
clus                 M0  M1  MX
  6P LOSS CNV         5   1   1
  6P LOSS WILD-TYPE 113  15   7
D46V7, multiclass
    clus
vv   6P LOSS CNV 6P LOSS WILD-TYPE
  M0           5               113
  M1           1                15
  MX           1                 7
                   vv
clus                 I II III IV
  6P LOSS CNV        1  0   3  1
  6P LOSS WILD-TYPE 23 37  36 25
D46V8, multiclass
     clus
vv    6P LOSS CNV 6P LOSS WILD-TYPE
  I             1                23
  II            0                37
  III           3                36
  IV            1                25
D46V9, binary
[1] "tbl2"
                   cls
clus                [,1] [,2]
  6P LOSS CNV          0    9
  6P LOSS WILD-TYPE    5  166
     clus
vv    6P LOSS CNV 6P LOSS WILD-TYPE
  NO            0                 5
  YES           9               166
                   vv
clus                 R0  R1  R2  RX
  6P LOSS CNV         7   0   0   2
  6P LOSS WILD-TYPE 118   7  12  23
D46V10, multiclass
    clus
vv   6P LOSS CNV 6P LOSS WILD-TYPE
  R0           7               118
  R1           0                 7
  R2           0                12
  RX           2                23
D46V11, continuous

Clustering(47) Variable = 6q loss
D47V1, survival
                   sevent
clus2                 0   1
  6Q LOSS CNV         9   1
  6Q LOSS WILD-TYPE 115  18
      6Q LOSS CNV 6Q LOSS WILD-TYPE 
               10               133 
      6Q LOSS CNV 6Q LOSS WILD-TYPE 
                1                18 
$`6Q LOSS CNV`
TCGA-BR-7722 TCGA-BR-A4J8 TCGA-BR-A4PF TCGA-CG-4443 TCGA-CG-5719 TCGA-CG-5725 
        0.16         0.23         0.72        29.98         1.02        15.02 
TCGA-D7-6520 TCGA-D7-6525 TCGA-D7-6815 TCGA-FP-8631 
        9.63         5.95         3.65         0.56 

$`6Q LOSS WILD-TYPE`
TCGA-B7-5816 TCGA-B7-5818 TCGA-BR-6452 TCGA-BR-6455 TCGA-BR-6457 TCGA-BR-6458 
        5.62         0.10         0.95         1.41         1.35         1.35 
TCGA-BR-6563 TCGA-BR-6564 TCGA-BR-6565 TCGA-BR-6566 TCGA-BR-6705 TCGA-BR-6706 
        0.85         0.82         0.62         0.62         1.71         2.17 
TCGA-BR-6707 TCGA-BR-6709 TCGA-BR-6710 TCGA-BR-6801 TCGA-BR-6802 TCGA-BR-6803 
        0.99         1.22         0.66         1.12         0.76         0.66 
TCGA-BR-6852 TCGA-BR-7196 TCGA-BR-7197 TCGA-BR-7703 TCGA-BR-7704 TCGA-BR-7707 
        0.26         1.22         1.48         0.46         1.25         0.13 
TCGA-BR-7715 TCGA-BR-7716 TCGA-BR-7717 TCGA-BR-7723 TCGA-BR-7851 TCGA-BR-7901 
        1.05         0.82         0.69         4.54         0.99         0.95 
TCGA-BR-7957 TCGA-BR-7958 TCGA-BR-7959 TCGA-BR-8059 TCGA-BR-8060 TCGA-BR-8077 
        0.69         0.16         1.08         0.82         1.32         0.69 
TCGA-BR-8078 TCGA-BR-8080 TCGA-BR-8081 TCGA-BR-8284 TCGA-BR-8285 TCGA-BR-8286 
        0.95         0.49         0.46         0.72         0.26         0.43 
TCGA-BR-8289 TCGA-BR-8291 TCGA-BR-8295 TCGA-BR-8296 TCGA-BR-8297 TCGA-BR-8592 
        0.26         1.18         1.55         1.48         0.76         0.20 
TCGA-BR-A4IU TCGA-BR-A4IV TCGA-BR-A4IY TCGA-BR-A4IZ TCGA-BR-A4J1 TCGA-BR-A4J2 
        0.59         0.92         0.39         0.79         0.72         0.79 
TCGA-BR-A4J4 TCGA-BR-A4J5 TCGA-BR-A4J6 TCGA-BR-A4J9 TCGA-BR-A4QI TCGA-BR-A4QL 
        0.53         0.43         0.13         0.10         0.49         2.24 
TCGA-CD-5798 TCGA-CD-5799 TCGA-CD-5800 TCGA-CD-5801 TCGA-CD-5802 TCGA-CD-5803 
        0.82         0.69         0.36         0.49         0.30         0.07 
TCGA-CG-4300 TCGA-CG-4301 TCGA-CG-4304 TCGA-CG-4305 TCGA-CG-4306 TCGA-CG-4436 
       20.02         3.02        27.02        15.95         1.02        52.96 
TCGA-CG-4437 TCGA-CG-4438 TCGA-CG-4440 TCGA-CG-4441 TCGA-CG-4444 TCGA-CG-4449 
        8.05        54.05         4.01        14.01        47.05        19.07 
TCGA-CG-4455 TCGA-CG-4460 TCGA-CG-4462 TCGA-CG-4465 TCGA-CG-4466 TCGA-CG-4469 
       12.03        21.99         1.02         8.98        18.94         7.07 
TCGA-CG-4472 TCGA-CG-4474 TCGA-CG-4477 TCGA-CG-5716 TCGA-CG-5717 TCGA-CG-5718 
       12.00         1.02         1.02         1.02         6.94         1.02 
TCGA-CG-5720 TCGA-CG-5721 TCGA-CG-5722 TCGA-CG-5723 TCGA-CG-5724 TCGA-CG-5726 
        0.99         5.98         0.95        70.06        12.03        28.96 
TCGA-CG-5727 TCGA-CG-5728 TCGA-CG-5730 TCGA-CG-5732 TCGA-CG-5733 TCGA-CG-5734 
       31.04        65.10         4.01        55.04        21.07         7.99 
TCGA-D7-5577 TCGA-D7-5578 TCGA-D7-5579 TCGA-D7-6518 TCGA-D7-6519 TCGA-D7-6521 
        8.65         3.58         4.54         9.80        15.65         8.19 
TCGA-D7-6522 TCGA-D7-6524 TCGA-D7-6526 TCGA-D7-6527 TCGA-D7-6528 TCGA-D7-6817 
        6.90         0.69         6.61         4.14         1.68         4.70 
TCGA-D7-6818 TCGA-D7-6820 TCGA-D7-6822 TCGA-EQ-5647 TCGA-EQ-8122 TCGA-F1-6177 
        4.04         2.93         4.27         0.62         7.79         6.54 
TCGA-F1-6874 TCGA-F1-6875 TCGA-FP-7735 TCGA-FP-7829 TCGA-FP-7916 TCGA-FP-7998 
        2.01        72.23         0.39         0.20         3.02         3.58 
TCGA-FP-8099 TCGA-FP-8209 TCGA-FP-8210 TCGA-HJ-7597 TCGA-IN-7806 TCGA-IN-7808 
        1.02        59.05         5.03        26.43         6.87         3.55 
TCGA-IP-7968 
        2.53 

      6Q LOSS CNV 6Q LOSS WILD-TYPE 
             0.16              0.07 
      6Q LOSS CNV 6Q LOSS WILD-TYPE 
            29.98             72.23 
      6Q LOSS CNV 6Q LOSS WILD-TYPE 
            2.335             1.250 
[1] "0.2 - 30.0 (2.3)" "0.1 - 72.2 (1.2)"
       TCGA-B7-5816        TCGA-B7-5818        TCGA-BR-6452        TCGA-BR-6455 
"6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" 
       TCGA-BR-6457        TCGA-BR-6458        TCGA-BR-6563        TCGA-BR-6564 
"6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" 
       TCGA-BR-6565        TCGA-BR-6566        TCGA-BR-6705        TCGA-BR-6706 
"6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" 
       TCGA-BR-6707        TCGA-BR-6709        TCGA-BR-6710        TCGA-BR-6801 
"6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" 
       TCGA-BR-6802        TCGA-BR-6803        TCGA-BR-6852        TCGA-BR-7196 
"6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" 
       TCGA-BR-7197        TCGA-BR-7703        TCGA-BR-7704        TCGA-BR-7707 
"6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" 
       TCGA-BR-7715        TCGA-BR-7716        TCGA-BR-7717        TCGA-BR-7722 
"6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE"       "6Q LOSS CNV" 
       TCGA-BR-7723        TCGA-BR-7851        TCGA-BR-7901        TCGA-BR-7957 
"6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" 
       TCGA-BR-7958        TCGA-BR-7959        TCGA-BR-8059        TCGA-BR-8060 
"6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" 
       TCGA-BR-8077        TCGA-BR-8078        TCGA-BR-8080        TCGA-BR-8081 
"6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" 
       TCGA-BR-8284        TCGA-BR-8285        TCGA-BR-8286        TCGA-BR-8289 
"6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" 
       TCGA-BR-8291        TCGA-BR-8295        TCGA-BR-8296        TCGA-BR-8297 
"6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" 
       TCGA-BR-8592        TCGA-BR-A4IU        TCGA-BR-A4IV        TCGA-BR-A4IY 
"6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" 
       TCGA-BR-A4IZ        TCGA-BR-A4J1        TCGA-BR-A4J2        TCGA-BR-A4J4 
"6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" 
       TCGA-BR-A4J5        TCGA-BR-A4J6        TCGA-BR-A4J8        TCGA-BR-A4J9 
"6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE"       "6Q LOSS CNV" "6Q LOSS WILD-TYPE" 
       TCGA-BR-A4PF        TCGA-BR-A4QI        TCGA-BR-A4QL        TCGA-CD-5798 
      "6Q LOSS CNV" "6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" 
       TCGA-CD-5799        TCGA-CD-5800        TCGA-CD-5801        TCGA-CD-5802 
"6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" 
       TCGA-CD-5803        TCGA-CG-4300        TCGA-CG-4301        TCGA-CG-4304 
"6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" 
       TCGA-CG-4305        TCGA-CG-4306        TCGA-CG-4436        TCGA-CG-4437 
"6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" 
       TCGA-CG-4438        TCGA-CG-4440        TCGA-CG-4441        TCGA-CG-4443 
"6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE"       "6Q LOSS CNV" 
       TCGA-CG-4444        TCGA-CG-4449        TCGA-CG-4455        TCGA-CG-4460 
"6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" 
       TCGA-CG-4462        TCGA-CG-4465        TCGA-CG-4466        TCGA-CG-4469 
"6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" 
       TCGA-CG-4472        TCGA-CG-4474        TCGA-CG-4477        TCGA-CG-5716 
"6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" 
       TCGA-CG-5717        TCGA-CG-5718        TCGA-CG-5719        TCGA-CG-5720 
"6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE"       "6Q LOSS CNV" "6Q LOSS WILD-TYPE" 
       TCGA-CG-5721        TCGA-CG-5722        TCGA-CG-5723        TCGA-CG-5724 
"6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" 
       TCGA-CG-5725        TCGA-CG-5726        TCGA-CG-5727        TCGA-CG-5728 
      "6Q LOSS CNV" "6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" 
       TCGA-CG-5730        TCGA-CG-5732        TCGA-CG-5733        TCGA-CG-5734 
"6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" 
       TCGA-D7-5577        TCGA-D7-5578        TCGA-D7-5579        TCGA-D7-6518 
"6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" 
       TCGA-D7-6519        TCGA-D7-6520        TCGA-D7-6521        TCGA-D7-6522 
"6Q LOSS WILD-TYPE"       "6Q LOSS CNV" "6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" 
       TCGA-D7-6524        TCGA-D7-6525        TCGA-D7-6526        TCGA-D7-6527 
"6Q LOSS WILD-TYPE"       "6Q LOSS CNV" "6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" 
       TCGA-D7-6528        TCGA-D7-6815        TCGA-D7-6817        TCGA-D7-6818 
"6Q LOSS WILD-TYPE"       "6Q LOSS CNV" "6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" 
       TCGA-D7-6820        TCGA-D7-6822        TCGA-EQ-5647        TCGA-EQ-8122 
"6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" 
       TCGA-F1-6177        TCGA-F1-6874        TCGA-F1-6875        TCGA-FP-7735 
"6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" 
       TCGA-FP-7829        TCGA-FP-7916        TCGA-FP-7998        TCGA-FP-8099 
"6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" 
       TCGA-FP-8209        TCGA-FP-8210        TCGA-FP-8631        TCGA-HJ-7597 
"6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE"       "6Q LOSS CNV" "6Q LOSS WILD-TYPE" 
       TCGA-IN-7806        TCGA-IN-7808        TCGA-IP-7968 
"6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" 
       TCGA-B7-5816        TCGA-B7-5818        TCGA-BR-6452        TCGA-BR-6455 
"6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" 
       TCGA-BR-6457        TCGA-BR-6458        TCGA-BR-6563        TCGA-BR-6564 
"6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" 
       TCGA-BR-6565        TCGA-BR-6566        TCGA-BR-6705        TCGA-BR-6706 
"6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" 
       TCGA-BR-6707        TCGA-BR-6709        TCGA-BR-6710        TCGA-BR-6801 
"6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" 
       TCGA-BR-6802        TCGA-BR-6803        TCGA-BR-6852        TCGA-BR-7196 
"6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" 
       TCGA-BR-7197        TCGA-BR-7703        TCGA-BR-7704        TCGA-BR-7707 
"6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" 
       TCGA-BR-7715        TCGA-BR-7716        TCGA-BR-7717        TCGA-BR-7722 
"6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE"       "6Q LOSS CNV" 
       TCGA-BR-7723        TCGA-BR-7851        TCGA-BR-7901        TCGA-BR-7957 
"6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" 
       TCGA-BR-7958        TCGA-BR-7959        TCGA-BR-8059        TCGA-BR-8060 
"6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" 
       TCGA-BR-8077        TCGA-BR-8078        TCGA-BR-8080        TCGA-BR-8081 
"6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" 
       TCGA-BR-8284        TCGA-BR-8285        TCGA-BR-8286        TCGA-BR-8289 
"6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" 
       TCGA-BR-8291        TCGA-BR-8295        TCGA-BR-8296        TCGA-BR-8297 
"6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" 
       TCGA-BR-8592        TCGA-BR-A4IU        TCGA-BR-A4IV        TCGA-BR-A4IY 
"6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" 
       TCGA-BR-A4IZ        TCGA-BR-A4J1        TCGA-BR-A4J2        TCGA-BR-A4J4 
"6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" 
       TCGA-BR-A4J5        TCGA-BR-A4J6        TCGA-BR-A4J8        TCGA-BR-A4J9 
"6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE"       "6Q LOSS CNV" "6Q LOSS WILD-TYPE" 
       TCGA-BR-A4PF        TCGA-BR-A4QI        TCGA-BR-A4QL        TCGA-CD-5798 
      "6Q LOSS CNV" "6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" 
       TCGA-CD-5799        TCGA-CD-5800        TCGA-CD-5801        TCGA-CD-5802 
"6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" 
       TCGA-CD-5803        TCGA-CG-4300        TCGA-CG-4301        TCGA-CG-4304 
"6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" 
       TCGA-CG-4305        TCGA-CG-4306        TCGA-CG-4436        TCGA-CG-4437 
"6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" 
       TCGA-CG-4438        TCGA-CG-4440        TCGA-CG-4441        TCGA-CG-4443 
"6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE"       "6Q LOSS CNV" 
       TCGA-CG-4444        TCGA-CG-4449        TCGA-CG-4455        TCGA-CG-4460 
"6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" 
       TCGA-CG-4462        TCGA-CG-4465        TCGA-CG-4466        TCGA-CG-4469 
"6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" 
       TCGA-CG-4472        TCGA-CG-4474        TCGA-CG-4477        TCGA-CG-5716 
"6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" 
       TCGA-CG-5717        TCGA-CG-5718        TCGA-CG-5719        TCGA-CG-5720 
"6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE"       "6Q LOSS CNV" "6Q LOSS WILD-TYPE" 
       TCGA-CG-5721        TCGA-CG-5722        TCGA-CG-5723        TCGA-CG-5724 
"6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" 
       TCGA-CG-5725        TCGA-CG-5726        TCGA-CG-5727        TCGA-CG-5728 
      "6Q LOSS CNV" "6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" 
       TCGA-CG-5730        TCGA-CG-5732        TCGA-CG-5733        TCGA-CG-5734 
"6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" 
       TCGA-D7-5577        TCGA-D7-5578        TCGA-D7-5579        TCGA-D7-6518 
"6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" 
       TCGA-D7-6519        TCGA-D7-6520        TCGA-D7-6521        TCGA-D7-6522 
"6Q LOSS WILD-TYPE"       "6Q LOSS CNV" "6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" 
       TCGA-D7-6524        TCGA-D7-6525        TCGA-D7-6526        TCGA-D7-6527 
"6Q LOSS WILD-TYPE"       "6Q LOSS CNV" "6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" 
       TCGA-D7-6528        TCGA-D7-6815        TCGA-D7-6817        TCGA-D7-6818 
"6Q LOSS WILD-TYPE"       "6Q LOSS CNV" "6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" 
       TCGA-D7-6820        TCGA-D7-6822        TCGA-EQ-5647        TCGA-EQ-8122 
"6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" 
       TCGA-F1-6177        TCGA-F1-6874        TCGA-F1-6875        TCGA-FP-7735 
"6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" 
       TCGA-FP-7829        TCGA-FP-7916        TCGA-FP-7998        TCGA-FP-8099 
"6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" 
       TCGA-FP-8209        TCGA-FP-8210        TCGA-FP-8631        TCGA-HJ-7597 
"6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE"       "6Q LOSS CNV" "6Q LOSS WILD-TYPE" 
       TCGA-IN-7806        TCGA-IN-7808        TCGA-IP-7968 
"6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" 
       TCGA-B7-5816        TCGA-B7-5818        TCGA-BR-6452        TCGA-BR-6455 
"6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" 
       TCGA-BR-6457        TCGA-BR-6458        TCGA-BR-6563        TCGA-BR-6564 
"6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" 
       TCGA-BR-6565        TCGA-BR-6566        TCGA-BR-6705        TCGA-BR-6706 
"6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" 
       TCGA-BR-6707        TCGA-BR-6709        TCGA-BR-6710        TCGA-BR-6801 
"6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" 
       TCGA-BR-6802        TCGA-BR-6803        TCGA-BR-6852        TCGA-BR-7196 
"6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" 
       TCGA-BR-7197        TCGA-BR-7703        TCGA-BR-7704        TCGA-BR-7707 
"6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" 
       TCGA-BR-7715        TCGA-BR-7716        TCGA-BR-7717        TCGA-BR-7722 
"6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE"       "6Q LOSS CNV" 
       TCGA-BR-7723        TCGA-BR-7851        TCGA-BR-7901        TCGA-BR-7957 
"6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" 
       TCGA-BR-7958        TCGA-BR-7959        TCGA-BR-8059        TCGA-BR-8060 
"6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" 
       TCGA-BR-8077        TCGA-BR-8078        TCGA-BR-8080        TCGA-BR-8081 
"6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" 
       TCGA-BR-8284        TCGA-BR-8285        TCGA-BR-8286        TCGA-BR-8289 
"6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" 
       TCGA-BR-8291        TCGA-BR-8295        TCGA-BR-8296        TCGA-BR-8297 
"6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" 
       TCGA-BR-8592        TCGA-BR-A4IU        TCGA-BR-A4IV        TCGA-BR-A4IY 
"6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" 
       TCGA-BR-A4IZ        TCGA-BR-A4J1        TCGA-BR-A4J2        TCGA-BR-A4J4 
"6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" 
       TCGA-BR-A4J5        TCGA-BR-A4J6        TCGA-BR-A4J8        TCGA-BR-A4J9 
"6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE"       "6Q LOSS CNV" "6Q LOSS WILD-TYPE" 
       TCGA-BR-A4PF        TCGA-BR-A4QI        TCGA-BR-A4QL        TCGA-CD-5798 
      "6Q LOSS CNV" "6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" 
       TCGA-CD-5799        TCGA-CD-5800        TCGA-CD-5801        TCGA-CD-5802 
"6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" 
       TCGA-CD-5803        TCGA-CG-4300        TCGA-CG-4301        TCGA-CG-4304 
"6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" 
       TCGA-CG-4305        TCGA-CG-4306        TCGA-CG-4436        TCGA-CG-4437 
"6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" 
       TCGA-CG-4438        TCGA-CG-4440        TCGA-CG-4441        TCGA-CG-4443 
"6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE"       "6Q LOSS CNV" 
       TCGA-CG-4444        TCGA-CG-4449        TCGA-CG-4455        TCGA-CG-4460 
"6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" 
       TCGA-CG-4462        TCGA-CG-4465        TCGA-CG-4466        TCGA-CG-4469 
"6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" 
       TCGA-CG-4472        TCGA-CG-4474        TCGA-CG-4477        TCGA-CG-5716 
"6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" 
       TCGA-CG-5717        TCGA-CG-5718        TCGA-CG-5719        TCGA-CG-5720 
"6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE"       "6Q LOSS CNV" "6Q LOSS WILD-TYPE" 
       TCGA-CG-5721        TCGA-CG-5722        TCGA-CG-5723        TCGA-CG-5724 
"6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" 
       TCGA-CG-5725        TCGA-CG-5726        TCGA-CG-5727        TCGA-CG-5728 
      "6Q LOSS CNV" "6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" 
       TCGA-CG-5730        TCGA-CG-5732        TCGA-CG-5733        TCGA-CG-5734 
"6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" 
       TCGA-D7-5577        TCGA-D7-5578        TCGA-D7-5579        TCGA-D7-6518 
"6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" 
       TCGA-D7-6519        TCGA-D7-6520        TCGA-D7-6521        TCGA-D7-6522 
"6Q LOSS WILD-TYPE"       "6Q LOSS CNV" "6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" 
       TCGA-D7-6524        TCGA-D7-6525        TCGA-D7-6526        TCGA-D7-6527 
"6Q LOSS WILD-TYPE"       "6Q LOSS CNV" "6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" 
       TCGA-D7-6528        TCGA-D7-6815        TCGA-D7-6817        TCGA-D7-6818 
"6Q LOSS WILD-TYPE"       "6Q LOSS CNV" "6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" 
       TCGA-D7-6820        TCGA-D7-6822        TCGA-EQ-5647        TCGA-EQ-8122 
"6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" 
       TCGA-F1-6177        TCGA-F1-6874        TCGA-F1-6875        TCGA-FP-7735 
"6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" 
       TCGA-FP-7829        TCGA-FP-7916        TCGA-FP-7998        TCGA-FP-8099 
"6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" 
       TCGA-FP-8209        TCGA-FP-8210        TCGA-FP-8631        TCGA-HJ-7597 
"6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE"       "6Q LOSS CNV" "6Q LOSS WILD-TYPE" 
       TCGA-IN-7806        TCGA-IN-7808        TCGA-IP-7968 
"6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" 
[1] "hr=" "1.4"
D47V2, continuous
D47V3, binary
[1] "tbl2"
                   cls
clus                [,1] [,2]
  6Q LOSS CNV          4   10
  6Q LOSS WILD-TYPE   68   98
        clus
vv       6Q LOSS CNV 6Q LOSS WILD-TYPE
  FEMALE           4                68
  MALE            10                98
                   vv
clus                STOMACH  ADENOCARCINOMA  DIFFUSE TYPE
  6Q LOSS CNV                                           0
  6Q LOSS WILD-TYPE                                    10
                   vv
clus                STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  6Q LOSS CNV                                                            2
  6Q LOSS WILD-TYPE                                                     14
                   vv
clus                STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  6Q LOSS CNV                                                                       1
  6Q LOSS WILD-TYPE                                                                 7
                   vv
clus                STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE
  6Q LOSS CNV                                                              0
  6Q LOSS WILD-TYPE                                                        3
                   vv
clus                STOMACH ADENOCARCINOMA  SIGNET RING TYPE
  6Q LOSS CNV                                              0
  6Q LOSS WILD-TYPE                                        1
                   vv
clus                STOMACH ADENOCARCINOMA - DIFFUSE TYPE
  6Q LOSS CNV                                           1
  6Q LOSS WILD-TYPE                                    15
                   vv
clus                STOMACH ADENOCARCINOMA - NOT OTHERWISE SPECIFIED (NOS)
  6Q LOSS CNV                                                            5
  6Q LOSS WILD-TYPE                                                     68
                   vv
clus                STOMACH INTESTINAL ADENOCARCINOMA - MUCINOUS TYPE
  6Q LOSS CNV                                                       0
  6Q LOSS WILD-TYPE                                                 7
                   vv
clus                STOMACH INTESTINAL ADENOCARCINOMA - PAPILLARY TYPE
  6Q LOSS CNV                                                        0
  6Q LOSS WILD-TYPE                                                  3
                   vv
clus                STOMACH INTESTINAL ADENOCARCINOMA - TUBULAR TYPE
  6Q LOSS CNV                                                      3
  6Q LOSS WILD-TYPE                                                7
                   vv
clus                STOMACH INTESTINAL ADENOCARCINOMA - TYPE NOT OTHERWISE SPECIFIED (NOS)
  6Q LOSS CNV                                                                            2
  6Q LOSS WILD-TYPE                                                                     26
D47V4, multiclass
                   vv
clus                T1 T2 T3 T4
  6Q LOSS CNV        1  6  3  1
  6Q LOSS WILD-TYPE  5 46 53 17
D47V5, multiclass
    clus
vv   6Q LOSS CNV 6Q LOSS WILD-TYPE
  T1           1                 5
  T2           6                46
  T3           3                53
  T4           1                17
                   vv
clus                N0 N1 N2 N3
  6Q LOSS CNV        4  2  3  0
  6Q LOSS WILD-TYPE 40 47 20 15
D47V6, multiclass
    clus
vv   6Q LOSS CNV 6Q LOSS WILD-TYPE
  N0           4                40
  N1           2                47
  N2           3                20
  N3           0                15
                   vv
clus                 M0  M1  MX
  6Q LOSS CNV         9   1   1
  6Q LOSS WILD-TYPE 109  15   7
D47V7, multiclass
    clus
vv   6Q LOSS CNV 6Q LOSS WILD-TYPE
  M0           9               109
  M1           1                15
  MX           1                 7
                   vv
clus                 I II III IV
  6Q LOSS CNV        3  0   5  1
  6Q LOSS WILD-TYPE 21 37  34 25
D47V8, multiclass
     clus
vv    6Q LOSS CNV 6Q LOSS WILD-TYPE
  I             3                21
  II            0                37
  III           5                34
  IV            1                25
D47V9, binary
[1] "tbl2"
                   cls
clus                [,1] [,2]
  6Q LOSS CNV          0   14
  6Q LOSS WILD-TYPE    5  161
     clus
vv    6Q LOSS CNV 6Q LOSS WILD-TYPE
  NO            0                 5
  YES          14               161
                   vv
clus                 R0  R1  R2  RX
  6Q LOSS CNV        11   0   0   3
  6Q LOSS WILD-TYPE 114   7  12  22
D47V10, multiclass
    clus
vv   6Q LOSS CNV 6Q LOSS WILD-TYPE
  R0          11               114
  R1           0                 7
  R2           0                12
  RX           3                22
D47V11, continuous

Clustering(48) Variable = 7p loss
D48V1, survival
                   sevent
clus2                 0   1
  7P LOSS CNV         3   0
  7P LOSS WILD-TYPE 121  19
      7P LOSS CNV 7P LOSS WILD-TYPE 
                3               140 
      7P LOSS CNV 7P LOSS WILD-TYPE 
                0                19 
$`7P LOSS CNV`
TCGA-BR-7723 TCGA-CG-4438 TCGA-CG-4443 
        4.54        54.05        29.98 

$`7P LOSS WILD-TYPE`
TCGA-B7-5816 TCGA-B7-5818 TCGA-BR-6452 TCGA-BR-6455 TCGA-BR-6457 TCGA-BR-6458 
        5.62         0.10         0.95         1.41         1.35         1.35 
TCGA-BR-6563 TCGA-BR-6564 TCGA-BR-6565 TCGA-BR-6566 TCGA-BR-6705 TCGA-BR-6706 
        0.85         0.82         0.62         0.62         1.71         2.17 
TCGA-BR-6707 TCGA-BR-6709 TCGA-BR-6710 TCGA-BR-6801 TCGA-BR-6802 TCGA-BR-6803 
        0.99         1.22         0.66         1.12         0.76         0.66 
TCGA-BR-6852 TCGA-BR-7196 TCGA-BR-7197 TCGA-BR-7703 TCGA-BR-7704 TCGA-BR-7707 
        0.26         1.22         1.48         0.46         1.25         0.13 
TCGA-BR-7715 TCGA-BR-7716 TCGA-BR-7717 TCGA-BR-7722 TCGA-BR-7851 TCGA-BR-7901 
        1.05         0.82         0.69         0.16         0.99         0.95 
TCGA-BR-7957 TCGA-BR-7958 TCGA-BR-7959 TCGA-BR-8059 TCGA-BR-8060 TCGA-BR-8077 
        0.69         0.16         1.08         0.82         1.32         0.69 
TCGA-BR-8078 TCGA-BR-8080 TCGA-BR-8081 TCGA-BR-8284 TCGA-BR-8285 TCGA-BR-8286 
        0.95         0.49         0.46         0.72         0.26         0.43 
TCGA-BR-8289 TCGA-BR-8291 TCGA-BR-8295 TCGA-BR-8296 TCGA-BR-8297 TCGA-BR-8592 
        0.26         1.18         1.55         1.48         0.76         0.20 
TCGA-BR-A4IU TCGA-BR-A4IV TCGA-BR-A4IY TCGA-BR-A4IZ TCGA-BR-A4J1 TCGA-BR-A4J2 
        0.59         0.92         0.39         0.79         0.72         0.79 
TCGA-BR-A4J4 TCGA-BR-A4J5 TCGA-BR-A4J6 TCGA-BR-A4J8 TCGA-BR-A4J9 TCGA-BR-A4PF 
        0.53         0.43         0.13         0.23         0.10         0.72 
TCGA-BR-A4QI TCGA-BR-A4QL TCGA-CD-5798 TCGA-CD-5799 TCGA-CD-5800 TCGA-CD-5801 
        0.49         2.24         0.82         0.69         0.36         0.49 
TCGA-CD-5802 TCGA-CD-5803 TCGA-CG-4300 TCGA-CG-4301 TCGA-CG-4304 TCGA-CG-4305 
        0.30         0.07        20.02         3.02        27.02        15.95 
TCGA-CG-4306 TCGA-CG-4436 TCGA-CG-4437 TCGA-CG-4440 TCGA-CG-4441 TCGA-CG-4444 
        1.02        52.96         8.05         4.01        14.01        47.05 
TCGA-CG-4449 TCGA-CG-4455 TCGA-CG-4460 TCGA-CG-4462 TCGA-CG-4465 TCGA-CG-4466 
       19.07        12.03        21.99         1.02         8.98        18.94 
TCGA-CG-4469 TCGA-CG-4472 TCGA-CG-4474 TCGA-CG-4477 TCGA-CG-5716 TCGA-CG-5717 
        7.07        12.00         1.02         1.02         1.02         6.94 
TCGA-CG-5718 TCGA-CG-5719 TCGA-CG-5720 TCGA-CG-5721 TCGA-CG-5722 TCGA-CG-5723 
        1.02         1.02         0.99         5.98         0.95        70.06 
TCGA-CG-5724 TCGA-CG-5725 TCGA-CG-5726 TCGA-CG-5727 TCGA-CG-5728 TCGA-CG-5730 
       12.03        15.02        28.96        31.04        65.10         4.01 
TCGA-CG-5732 TCGA-CG-5733 TCGA-CG-5734 TCGA-D7-5577 TCGA-D7-5578 TCGA-D7-5579 
       55.04        21.07         7.99         8.65         3.58         4.54 
TCGA-D7-6518 TCGA-D7-6519 TCGA-D7-6520 TCGA-D7-6521 TCGA-D7-6522 TCGA-D7-6524 
        9.80        15.65         9.63         8.19         6.90         0.69 
TCGA-D7-6525 TCGA-D7-6526 TCGA-D7-6527 TCGA-D7-6528 TCGA-D7-6815 TCGA-D7-6817 
        5.95         6.61         4.14         1.68         3.65         4.70 
TCGA-D7-6818 TCGA-D7-6820 TCGA-D7-6822 TCGA-EQ-5647 TCGA-EQ-8122 TCGA-F1-6177 
        4.04         2.93         4.27         0.62         7.79         6.54 
TCGA-F1-6874 TCGA-F1-6875 TCGA-FP-7735 TCGA-FP-7829 TCGA-FP-7916 TCGA-FP-7998 
        2.01        72.23         0.39         0.20         3.02         3.58 
TCGA-FP-8099 TCGA-FP-8209 TCGA-FP-8210 TCGA-FP-8631 TCGA-HJ-7597 TCGA-IN-7806 
        1.02        59.05         5.03         0.56        26.43         6.87 
TCGA-IN-7808 TCGA-IP-7968 
        3.55         2.53 

      7P LOSS CNV 7P LOSS WILD-TYPE 
             4.54              0.07 
      7P LOSS CNV 7P LOSS WILD-TYPE 
            54.05             72.23 
      7P LOSS CNV 7P LOSS WILD-TYPE 
            29.98              1.22 
[1] "4.5 - 54.0 (30.0)" "0.1 - 72.2 (1.2)" 
       TCGA-B7-5816        TCGA-B7-5818        TCGA-BR-6452        TCGA-BR-6455 
"7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" 
       TCGA-BR-6457        TCGA-BR-6458        TCGA-BR-6563        TCGA-BR-6564 
"7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" 
       TCGA-BR-6565        TCGA-BR-6566        TCGA-BR-6705        TCGA-BR-6706 
"7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" 
       TCGA-BR-6707        TCGA-BR-6709        TCGA-BR-6710        TCGA-BR-6801 
"7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" 
       TCGA-BR-6802        TCGA-BR-6803        TCGA-BR-6852        TCGA-BR-7196 
"7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" 
       TCGA-BR-7197        TCGA-BR-7703        TCGA-BR-7704        TCGA-BR-7707 
"7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" 
       TCGA-BR-7715        TCGA-BR-7716        TCGA-BR-7717        TCGA-BR-7722 
"7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" 
       TCGA-BR-7723        TCGA-BR-7851        TCGA-BR-7901        TCGA-BR-7957 
      "7P LOSS CNV" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" 
       TCGA-BR-7958        TCGA-BR-7959        TCGA-BR-8059        TCGA-BR-8060 
"7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" 
       TCGA-BR-8077        TCGA-BR-8078        TCGA-BR-8080        TCGA-BR-8081 
"7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" 
       TCGA-BR-8284        TCGA-BR-8285        TCGA-BR-8286        TCGA-BR-8289 
"7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" 
       TCGA-BR-8291        TCGA-BR-8295        TCGA-BR-8296        TCGA-BR-8297 
"7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" 
       TCGA-BR-8592        TCGA-BR-A4IU        TCGA-BR-A4IV        TCGA-BR-A4IY 
"7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" 
       TCGA-BR-A4IZ        TCGA-BR-A4J1        TCGA-BR-A4J2        TCGA-BR-A4J4 
"7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" 
       TCGA-BR-A4J5        TCGA-BR-A4J6        TCGA-BR-A4J8        TCGA-BR-A4J9 
"7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" 
       TCGA-BR-A4PF        TCGA-BR-A4QI        TCGA-BR-A4QL        TCGA-CD-5798 
"7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" 
       TCGA-CD-5799        TCGA-CD-5800        TCGA-CD-5801        TCGA-CD-5802 
"7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" 
       TCGA-CD-5803        TCGA-CG-4300        TCGA-CG-4301        TCGA-CG-4304 
"7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" 
       TCGA-CG-4305        TCGA-CG-4306        TCGA-CG-4436        TCGA-CG-4437 
"7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" 
       TCGA-CG-4438        TCGA-CG-4440        TCGA-CG-4441        TCGA-CG-4443 
      "7P LOSS CNV" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE"       "7P LOSS CNV" 
       TCGA-CG-4444        TCGA-CG-4449        TCGA-CG-4455        TCGA-CG-4460 
"7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" 
       TCGA-CG-4462        TCGA-CG-4465        TCGA-CG-4466        TCGA-CG-4469 
"7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" 
       TCGA-CG-4472        TCGA-CG-4474        TCGA-CG-4477        TCGA-CG-5716 
"7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" 
       TCGA-CG-5717        TCGA-CG-5718        TCGA-CG-5719        TCGA-CG-5720 
"7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" 
       TCGA-CG-5721        TCGA-CG-5722        TCGA-CG-5723        TCGA-CG-5724 
"7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" 
       TCGA-CG-5725        TCGA-CG-5726        TCGA-CG-5727        TCGA-CG-5728 
"7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" 
       TCGA-CG-5730        TCGA-CG-5732        TCGA-CG-5733        TCGA-CG-5734 
"7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" 
       TCGA-D7-5577        TCGA-D7-5578        TCGA-D7-5579        TCGA-D7-6518 
"7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" 
       TCGA-D7-6519        TCGA-D7-6520        TCGA-D7-6521        TCGA-D7-6522 
"7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" 
       TCGA-D7-6524        TCGA-D7-6525        TCGA-D7-6526        TCGA-D7-6527 
"7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" 
       TCGA-D7-6528        TCGA-D7-6815        TCGA-D7-6817        TCGA-D7-6818 
"7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" 
       TCGA-D7-6820        TCGA-D7-6822        TCGA-EQ-5647        TCGA-EQ-8122 
"7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" 
       TCGA-F1-6177        TCGA-F1-6874        TCGA-F1-6875        TCGA-FP-7735 
"7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" 
       TCGA-FP-7829        TCGA-FP-7916        TCGA-FP-7998        TCGA-FP-8099 
"7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" 
       TCGA-FP-8209        TCGA-FP-8210        TCGA-FP-8631        TCGA-HJ-7597 
"7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" 
       TCGA-IN-7806        TCGA-IN-7808        TCGA-IP-7968 
"7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" 
       TCGA-B7-5816        TCGA-B7-5818        TCGA-BR-6452        TCGA-BR-6455 
"7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" 
       TCGA-BR-6457        TCGA-BR-6458        TCGA-BR-6563        TCGA-BR-6564 
"7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" 
       TCGA-BR-6565        TCGA-BR-6566        TCGA-BR-6705        TCGA-BR-6706 
"7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" 
       TCGA-BR-6707        TCGA-BR-6709        TCGA-BR-6710        TCGA-BR-6801 
"7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" 
       TCGA-BR-6802        TCGA-BR-6803        TCGA-BR-6852        TCGA-BR-7196 
"7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" 
       TCGA-BR-7197        TCGA-BR-7703        TCGA-BR-7704        TCGA-BR-7707 
"7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" 
       TCGA-BR-7715        TCGA-BR-7716        TCGA-BR-7717        TCGA-BR-7722 
"7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" 
       TCGA-BR-7723        TCGA-BR-7851        TCGA-BR-7901        TCGA-BR-7957 
      "7P LOSS CNV" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" 
       TCGA-BR-7958        TCGA-BR-7959        TCGA-BR-8059        TCGA-BR-8060 
"7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" 
       TCGA-BR-8077        TCGA-BR-8078        TCGA-BR-8080        TCGA-BR-8081 
"7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" 
       TCGA-BR-8284        TCGA-BR-8285        TCGA-BR-8286        TCGA-BR-8289 
"7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" 
       TCGA-BR-8291        TCGA-BR-8295        TCGA-BR-8296        TCGA-BR-8297 
"7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" 
       TCGA-BR-8592        TCGA-BR-A4IU        TCGA-BR-A4IV        TCGA-BR-A4IY 
"7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" 
       TCGA-BR-A4IZ        TCGA-BR-A4J1        TCGA-BR-A4J2        TCGA-BR-A4J4 
"7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" 
       TCGA-BR-A4J5        TCGA-BR-A4J6        TCGA-BR-A4J8        TCGA-BR-A4J9 
"7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" 
       TCGA-BR-A4PF        TCGA-BR-A4QI        TCGA-BR-A4QL        TCGA-CD-5798 
"7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" 
       TCGA-CD-5799        TCGA-CD-5800        TCGA-CD-5801        TCGA-CD-5802 
"7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" 
       TCGA-CD-5803        TCGA-CG-4300        TCGA-CG-4301        TCGA-CG-4304 
"7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" 
       TCGA-CG-4305        TCGA-CG-4306        TCGA-CG-4436        TCGA-CG-4437 
"7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" 
       TCGA-CG-4438        TCGA-CG-4440        TCGA-CG-4441        TCGA-CG-4443 
      "7P LOSS CNV" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE"       "7P LOSS CNV" 
       TCGA-CG-4444        TCGA-CG-4449        TCGA-CG-4455        TCGA-CG-4460 
"7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" 
       TCGA-CG-4462        TCGA-CG-4465        TCGA-CG-4466        TCGA-CG-4469 
"7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" 
       TCGA-CG-4472        TCGA-CG-4474        TCGA-CG-4477        TCGA-CG-5716 
"7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" 
       TCGA-CG-5717        TCGA-CG-5718        TCGA-CG-5719        TCGA-CG-5720 
"7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" 
       TCGA-CG-5721        TCGA-CG-5722        TCGA-CG-5723        TCGA-CG-5724 
"7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" 
       TCGA-CG-5725        TCGA-CG-5726        TCGA-CG-5727        TCGA-CG-5728 
"7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" 
       TCGA-CG-5730        TCGA-CG-5732        TCGA-CG-5733        TCGA-CG-5734 
"7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" 
       TCGA-D7-5577        TCGA-D7-5578        TCGA-D7-5579        TCGA-D7-6518 
"7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" 
       TCGA-D7-6519        TCGA-D7-6520        TCGA-D7-6521        TCGA-D7-6522 
"7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" 
       TCGA-D7-6524        TCGA-D7-6525        TCGA-D7-6526        TCGA-D7-6527 
"7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" 
       TCGA-D7-6528        TCGA-D7-6815        TCGA-D7-6817        TCGA-D7-6818 
"7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" 
       TCGA-D7-6820        TCGA-D7-6822        TCGA-EQ-5647        TCGA-EQ-8122 
"7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" 
       TCGA-F1-6177        TCGA-F1-6874        TCGA-F1-6875        TCGA-FP-7735 
"7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" 
       TCGA-FP-7829        TCGA-FP-7916        TCGA-FP-7998        TCGA-FP-8099 
"7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" 
       TCGA-FP-8209        TCGA-FP-8210        TCGA-FP-8631        TCGA-HJ-7597 
"7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" 
       TCGA-IN-7806        TCGA-IN-7808        TCGA-IP-7968 
"7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" 
       TCGA-B7-5816        TCGA-B7-5818        TCGA-BR-6452        TCGA-BR-6455 
"7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" 
       TCGA-BR-6457        TCGA-BR-6458        TCGA-BR-6563        TCGA-BR-6564 
"7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" 
       TCGA-BR-6565        TCGA-BR-6566        TCGA-BR-6705        TCGA-BR-6706 
"7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" 
       TCGA-BR-6707        TCGA-BR-6709        TCGA-BR-6710        TCGA-BR-6801 
"7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" 
       TCGA-BR-6802        TCGA-BR-6803        TCGA-BR-6852        TCGA-BR-7196 
"7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" 
       TCGA-BR-7197        TCGA-BR-7703        TCGA-BR-7704        TCGA-BR-7707 
"7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" 
       TCGA-BR-7715        TCGA-BR-7716        TCGA-BR-7717        TCGA-BR-7722 
"7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" 
       TCGA-BR-7723        TCGA-BR-7851        TCGA-BR-7901        TCGA-BR-7957 
      "7P LOSS CNV" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" 
       TCGA-BR-7958        TCGA-BR-7959        TCGA-BR-8059        TCGA-BR-8060 
"7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" 
       TCGA-BR-8077        TCGA-BR-8078        TCGA-BR-8080        TCGA-BR-8081 
"7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" 
       TCGA-BR-8284        TCGA-BR-8285        TCGA-BR-8286        TCGA-BR-8289 
"7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" 
       TCGA-BR-8291        TCGA-BR-8295        TCGA-BR-8296        TCGA-BR-8297 
"7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" 
       TCGA-BR-8592        TCGA-BR-A4IU        TCGA-BR-A4IV        TCGA-BR-A4IY 
"7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" 
       TCGA-BR-A4IZ        TCGA-BR-A4J1        TCGA-BR-A4J2        TCGA-BR-A4J4 
"7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" 
       TCGA-BR-A4J5        TCGA-BR-A4J6        TCGA-BR-A4J8        TCGA-BR-A4J9 
"7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" 
       TCGA-BR-A4PF        TCGA-BR-A4QI        TCGA-BR-A4QL        TCGA-CD-5798 
"7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" 
       TCGA-CD-5799        TCGA-CD-5800        TCGA-CD-5801        TCGA-CD-5802 
"7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" 
       TCGA-CD-5803        TCGA-CG-4300        TCGA-CG-4301        TCGA-CG-4304 
"7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" 
       TCGA-CG-4305        TCGA-CG-4306        TCGA-CG-4436        TCGA-CG-4437 
"7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" 
       TCGA-CG-4438        TCGA-CG-4440        TCGA-CG-4441        TCGA-CG-4443 
      "7P LOSS CNV" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE"       "7P LOSS CNV" 
       TCGA-CG-4444        TCGA-CG-4449        TCGA-CG-4455        TCGA-CG-4460 
"7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" 
       TCGA-CG-4462        TCGA-CG-4465        TCGA-CG-4466        TCGA-CG-4469 
"7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" 
       TCGA-CG-4472        TCGA-CG-4474        TCGA-CG-4477        TCGA-CG-5716 
"7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" 
       TCGA-CG-5717        TCGA-CG-5718        TCGA-CG-5719        TCGA-CG-5720 
"7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" 
       TCGA-CG-5721        TCGA-CG-5722        TCGA-CG-5723        TCGA-CG-5724 
"7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" 
       TCGA-CG-5725        TCGA-CG-5726        TCGA-CG-5727        TCGA-CG-5728 
"7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" 
       TCGA-CG-5730        TCGA-CG-5732        TCGA-CG-5733        TCGA-CG-5734 
"7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" 
       TCGA-D7-5577        TCGA-D7-5578        TCGA-D7-5579        TCGA-D7-6518 
"7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" 
       TCGA-D7-6519        TCGA-D7-6520        TCGA-D7-6521        TCGA-D7-6522 
"7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" 
       TCGA-D7-6524        TCGA-D7-6525        TCGA-D7-6526        TCGA-D7-6527 
"7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" 
       TCGA-D7-6528        TCGA-D7-6815        TCGA-D7-6817        TCGA-D7-6818 
"7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" 
       TCGA-D7-6820        TCGA-D7-6822        TCGA-EQ-5647        TCGA-EQ-8122 
"7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" 
       TCGA-F1-6177        TCGA-F1-6874        TCGA-F1-6875        TCGA-FP-7735 
"7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" 
       TCGA-FP-7829        TCGA-FP-7916        TCGA-FP-7998        TCGA-FP-8099 
"7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" 
       TCGA-FP-8209        TCGA-FP-8210        TCGA-FP-8631        TCGA-HJ-7597 
"7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" 
       TCGA-IN-7806        TCGA-IN-7808        TCGA-IP-7968 
"7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" 
[1] "hr="     "7.9e+07"
D48V2, continuous
D48V3, binary
[1] "tbl2"
                   cls
clus                [,1] [,2]
  7P LOSS CNV          0    3
  7P LOSS WILD-TYPE   72  105
        clus
vv       7P LOSS CNV 7P LOSS WILD-TYPE
  FEMALE           0                72
  MALE             3               105
                   vv
clus                STOMACH  ADENOCARCINOMA  DIFFUSE TYPE
  7P LOSS CNV                                           0
  7P LOSS WILD-TYPE                                    10
                   vv
clus                STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  7P LOSS CNV                                                            0
  7P LOSS WILD-TYPE                                                     16
                   vv
clus                STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  7P LOSS CNV                                                                       0
  7P LOSS WILD-TYPE                                                                 8
                   vv
clus                STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE
  7P LOSS CNV                                                              0
  7P LOSS WILD-TYPE                                                        3
                   vv
clus                STOMACH ADENOCARCINOMA  SIGNET RING TYPE
  7P LOSS CNV                                              0
  7P LOSS WILD-TYPE                                        1
                   vv
clus                STOMACH ADENOCARCINOMA - DIFFUSE TYPE
  7P LOSS CNV                                           0
  7P LOSS WILD-TYPE                                    16
                   vv
clus                STOMACH ADENOCARCINOMA - NOT OTHERWISE SPECIFIED (NOS)
  7P LOSS CNV                                                            1
  7P LOSS WILD-TYPE                                                     72
                   vv
clus                STOMACH INTESTINAL ADENOCARCINOMA - MUCINOUS TYPE
  7P LOSS CNV                                                       0
  7P LOSS WILD-TYPE                                                 7
                   vv
clus                STOMACH INTESTINAL ADENOCARCINOMA - PAPILLARY TYPE
  7P LOSS CNV                                                        0
  7P LOSS WILD-TYPE                                                  3
                   vv
clus                STOMACH INTESTINAL ADENOCARCINOMA - TUBULAR TYPE
  7P LOSS CNV                                                      0
  7P LOSS WILD-TYPE                                               10
                   vv
clus                STOMACH INTESTINAL ADENOCARCINOMA - TYPE NOT OTHERWISE SPECIFIED (NOS)
  7P LOSS CNV                                                                            2
  7P LOSS WILD-TYPE                                                                     26
D48V4, multiclass
                   vv
clus                T1 T2 T3 T4
  7P LOSS CNV        1  0  1  1
  7P LOSS WILD-TYPE  5 52 55 17
D48V5, multiclass
    clus
vv   7P LOSS CNV 7P LOSS WILD-TYPE
  T1           1                 5
  T2           0                52
  T3           1                55
  T4           1                17
                   vv
clus                N0 N1 N2 N3
  7P LOSS CNV        1  0  2  0
  7P LOSS WILD-TYPE 43 49 21 15
D48V6, multiclass
    clus
vv   7P LOSS CNV 7P LOSS WILD-TYPE
  N0           1                43
  N1           0                49
  N2           2                21
  N3           0                15
                   vv
clus                 M0  M1  MX
  7P LOSS CNV         3   0   0
  7P LOSS WILD-TYPE 115  16   8
D48V7, multiclass
    clus
vv   7P LOSS CNV 7P LOSS WILD-TYPE
  M0           3               115
  M1           0                16
  MX           0                 8
                   vv
clus                 I II III IV
  7P LOSS CNV        1  1   0  1
  7P LOSS WILD-TYPE 23 36  39 25
D48V8, multiclass
     clus
vv    7P LOSS CNV 7P LOSS WILD-TYPE
  I             1                23
  II            1                36
  III           0                39
  IV            1                25
D48V9, binary
[1] "tbl2"
                   cls
clus                [,1] [,2]
  7P LOSS CNV          0    3
  7P LOSS WILD-TYPE    5  172
     clus
vv    7P LOSS CNV 7P LOSS WILD-TYPE
  NO            0                 5
  YES           3               172
                   vv
clus                 R0  R1  R2  RX
  7P LOSS CNV         3   0   0   0
  7P LOSS WILD-TYPE 122   7  12  25
D48V10, multiclass
    clus
vv   7P LOSS CNV 7P LOSS WILD-TYPE
  R0           3               122
  R1           0                 7
  R2           0                12
  RX           0                25
D48V11, continuous
[1] "Remove cluster labels:" "7P LOSS CNV"           
clus
      7P LOSS CNV 7P LOSS WILD-TYPE 
                1               135 
       TCGA-B7-5816        TCGA-BR-4183        TCGA-BR-4184        TCGA-BR-4188 
"7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" 
       TCGA-BR-4191        TCGA-BR-4253        TCGA-BR-4255        TCGA-BR-4256 
"7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" 
       TCGA-BR-4267        TCGA-BR-4279        TCGA-BR-4280        TCGA-BR-4361 
"7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" 
       TCGA-BR-4362        TCGA-BR-4367        TCGA-BR-4368        TCGA-BR-6452 
"7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" 
       TCGA-BR-6453        TCGA-BR-6454        TCGA-BR-6455        TCGA-BR-6456 
"7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" 
       TCGA-BR-6457        TCGA-BR-6458        TCGA-BR-6563        TCGA-BR-6564 
"7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" 
       TCGA-BR-6565        TCGA-BR-6566        TCGA-BR-6705        TCGA-BR-6706 
"7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" 
       TCGA-BR-6707        TCGA-BR-6709        TCGA-BR-6710        TCGA-BR-6801 
"7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" 
       TCGA-BR-6802        TCGA-BR-6803        TCGA-BR-6852        TCGA-BR-7196 
"7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" 
       TCGA-BR-7197        TCGA-BR-7703        TCGA-BR-7704        TCGA-BR-7707 
"7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" 
       TCGA-BR-7715        TCGA-BR-7716        TCGA-BR-7717        TCGA-BR-7722 
"7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" 
       TCGA-BR-7851        TCGA-BR-7901        TCGA-BR-7957        TCGA-BR-7958 
"7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" 
       TCGA-BR-7959        TCGA-BR-8059        TCGA-BR-8060        TCGA-BR-8077 
"7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" 
       TCGA-BR-8078        TCGA-BR-8080        TCGA-BR-8081        TCGA-BR-8284 
"7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" 
       TCGA-BR-8285        TCGA-BR-8286        TCGA-BR-8289        TCGA-BR-8291 
"7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" 
       TCGA-BR-8295        TCGA-BR-8296        TCGA-BR-8297        TCGA-BR-8592 
"7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" 
       TCGA-BR-A4IU        TCGA-BR-A4IV        TCGA-BR-A4IY        TCGA-BR-A4IZ 
"7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" 
       TCGA-BR-A4J1        TCGA-BR-A4J2        TCGA-BR-A4J4        TCGA-BR-A4J5 
"7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" 
       TCGA-BR-A4J6        TCGA-BR-A4J8        TCGA-BR-A4J9        TCGA-BR-A4PF 
"7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" 
       TCGA-BR-A4QI        TCGA-BR-A4QL        TCGA-CD-5804        TCGA-CG-5717 
"7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" 
       TCGA-CG-5718        TCGA-CG-5719        TCGA-CG-5720        TCGA-CG-5721 
"7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" 
       TCGA-CG-5722        TCGA-CG-5723        TCGA-CG-5724        TCGA-CG-5725 
"7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" 
       TCGA-CG-5726        TCGA-CG-5727        TCGA-CG-5728        TCGA-CG-5730 
"7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" 
       TCGA-CG-5732        TCGA-CG-5733        TCGA-CG-5734        TCGA-D7-5577 
"7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" 
       TCGA-D7-5578        TCGA-D7-5579        TCGA-D7-6518        TCGA-D7-6519 
"7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" 
       TCGA-D7-6520        TCGA-D7-6521        TCGA-D7-6522        TCGA-D7-6524 
"7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" 
       TCGA-D7-6525        TCGA-D7-6526        TCGA-D7-6527        TCGA-D7-6528 
"7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" 
       TCGA-D7-6815        TCGA-D7-6817        TCGA-D7-6818        TCGA-D7-6820 
"7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" 
       TCGA-D7-6822        TCGA-EQ-5647        TCGA-EQ-8122        TCGA-F1-6177 
"7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" 
       TCGA-F1-6874        TCGA-F1-6875        TCGA-FP-7735        TCGA-FP-7829 
"7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" 
       TCGA-FP-7916        TCGA-FP-7998        TCGA-FP-8099        TCGA-FP-8209 
"7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" 
       TCGA-FP-8210        TCGA-FP-8631        TCGA-HF-7131        TCGA-HF-7132 
"7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" 
       TCGA-HF-7133        TCGA-HF-7134        TCGA-HF-7136        TCGA-HJ-7597 
"7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" 
       TCGA-IN-7806        TCGA-IN-7808        TCGA-IP-7968 
"7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" 

Clustering(49) Variable = 7q loss
D49V1, survival
                   sevent
clus2                 0   1
  7Q LOSS CNV         6   0
  7Q LOSS WILD-TYPE 118  19
      7Q LOSS CNV 7Q LOSS WILD-TYPE 
                6               137 
      7Q LOSS CNV 7Q LOSS WILD-TYPE 
                0                19 
$`7Q LOSS CNV`
TCGA-BR-7723 TCGA-CG-4438 TCGA-CG-4443 TCGA-D7-6820 TCGA-FP-7829 TCGA-FP-8631 
        4.54        54.05        29.98         2.93         0.20         0.56 

$`7Q LOSS WILD-TYPE`
TCGA-B7-5816 TCGA-B7-5818 TCGA-BR-6452 TCGA-BR-6455 TCGA-BR-6457 TCGA-BR-6458 
        5.62         0.10         0.95         1.41         1.35         1.35 
TCGA-BR-6563 TCGA-BR-6564 TCGA-BR-6565 TCGA-BR-6566 TCGA-BR-6705 TCGA-BR-6706 
        0.85         0.82         0.62         0.62         1.71         2.17 
TCGA-BR-6707 TCGA-BR-6709 TCGA-BR-6710 TCGA-BR-6801 TCGA-BR-6802 TCGA-BR-6803 
        0.99         1.22         0.66         1.12         0.76         0.66 
TCGA-BR-6852 TCGA-BR-7196 TCGA-BR-7197 TCGA-BR-7703 TCGA-BR-7704 TCGA-BR-7707 
        0.26         1.22         1.48         0.46         1.25         0.13 
TCGA-BR-7715 TCGA-BR-7716 TCGA-BR-7717 TCGA-BR-7722 TCGA-BR-7851 TCGA-BR-7901 
        1.05         0.82         0.69         0.16         0.99         0.95 
TCGA-BR-7957 TCGA-BR-7958 TCGA-BR-7959 TCGA-BR-8059 TCGA-BR-8060 TCGA-BR-8077 
        0.69         0.16         1.08         0.82         1.32         0.69 
TCGA-BR-8078 TCGA-BR-8080 TCGA-BR-8081 TCGA-BR-8284 TCGA-BR-8285 TCGA-BR-8286 
        0.95         0.49         0.46         0.72         0.26         0.43 
TCGA-BR-8289 TCGA-BR-8291 TCGA-BR-8295 TCGA-BR-8296 TCGA-BR-8297 TCGA-BR-8592 
        0.26         1.18         1.55         1.48         0.76         0.20 
TCGA-BR-A4IU TCGA-BR-A4IV TCGA-BR-A4IY TCGA-BR-A4IZ TCGA-BR-A4J1 TCGA-BR-A4J2 
        0.59         0.92         0.39         0.79         0.72         0.79 
TCGA-BR-A4J4 TCGA-BR-A4J5 TCGA-BR-A4J6 TCGA-BR-A4J8 TCGA-BR-A4J9 TCGA-BR-A4PF 
        0.53         0.43         0.13         0.23         0.10         0.72 
TCGA-BR-A4QI TCGA-BR-A4QL TCGA-CD-5798 TCGA-CD-5799 TCGA-CD-5800 TCGA-CD-5801 
        0.49         2.24         0.82         0.69         0.36         0.49 
TCGA-CD-5802 TCGA-CD-5803 TCGA-CG-4300 TCGA-CG-4301 TCGA-CG-4304 TCGA-CG-4305 
        0.30         0.07        20.02         3.02        27.02        15.95 
TCGA-CG-4306 TCGA-CG-4436 TCGA-CG-4437 TCGA-CG-4440 TCGA-CG-4441 TCGA-CG-4444 
        1.02        52.96         8.05         4.01        14.01        47.05 
TCGA-CG-4449 TCGA-CG-4455 TCGA-CG-4460 TCGA-CG-4462 TCGA-CG-4465 TCGA-CG-4466 
       19.07        12.03        21.99         1.02         8.98        18.94 
TCGA-CG-4469 TCGA-CG-4472 TCGA-CG-4474 TCGA-CG-4477 TCGA-CG-5716 TCGA-CG-5717 
        7.07        12.00         1.02         1.02         1.02         6.94 
TCGA-CG-5718 TCGA-CG-5719 TCGA-CG-5720 TCGA-CG-5721 TCGA-CG-5722 TCGA-CG-5723 
        1.02         1.02         0.99         5.98         0.95        70.06 
TCGA-CG-5724 TCGA-CG-5725 TCGA-CG-5726 TCGA-CG-5727 TCGA-CG-5728 TCGA-CG-5730 
       12.03        15.02        28.96        31.04        65.10         4.01 
TCGA-CG-5732 TCGA-CG-5733 TCGA-CG-5734 TCGA-D7-5577 TCGA-D7-5578 TCGA-D7-5579 
       55.04        21.07         7.99         8.65         3.58         4.54 
TCGA-D7-6518 TCGA-D7-6519 TCGA-D7-6520 TCGA-D7-6521 TCGA-D7-6522 TCGA-D7-6524 
        9.80        15.65         9.63         8.19         6.90         0.69 
TCGA-D7-6525 TCGA-D7-6526 TCGA-D7-6527 TCGA-D7-6528 TCGA-D7-6815 TCGA-D7-6817 
        5.95         6.61         4.14         1.68         3.65         4.70 
TCGA-D7-6818 TCGA-D7-6822 TCGA-EQ-5647 TCGA-EQ-8122 TCGA-F1-6177 TCGA-F1-6874 
        4.04         4.27         0.62         7.79         6.54         2.01 
TCGA-F1-6875 TCGA-FP-7735 TCGA-FP-7916 TCGA-FP-7998 TCGA-FP-8099 TCGA-FP-8209 
       72.23         0.39         3.02         3.58         1.02        59.05 
TCGA-FP-8210 TCGA-HJ-7597 TCGA-IN-7806 TCGA-IN-7808 TCGA-IP-7968 
        5.03        26.43         6.87         3.55         2.53 

      7Q LOSS CNV 7Q LOSS WILD-TYPE 
             0.20              0.07 
      7Q LOSS CNV 7Q LOSS WILD-TYPE 
            54.05             72.23 
      7Q LOSS CNV 7Q LOSS WILD-TYPE 
            3.735             1.220 
[1] "0.2 - 54.0 (3.7)" "0.1 - 72.2 (1.2)"
       TCGA-B7-5816        TCGA-B7-5818        TCGA-BR-6452        TCGA-BR-6455 
"7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" 
       TCGA-BR-6457        TCGA-BR-6458        TCGA-BR-6563        TCGA-BR-6564 
"7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" 
       TCGA-BR-6565        TCGA-BR-6566        TCGA-BR-6705        TCGA-BR-6706 
"7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" 
       TCGA-BR-6707        TCGA-BR-6709        TCGA-BR-6710        TCGA-BR-6801 
"7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" 
       TCGA-BR-6802        TCGA-BR-6803        TCGA-BR-6852        TCGA-BR-7196 
"7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" 
       TCGA-BR-7197        TCGA-BR-7703        TCGA-BR-7704        TCGA-BR-7707 
"7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" 
       TCGA-BR-7715        TCGA-BR-7716        TCGA-BR-7717        TCGA-BR-7722 
"7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" 
       TCGA-BR-7723        TCGA-BR-7851        TCGA-BR-7901        TCGA-BR-7957 
      "7Q LOSS CNV" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" 
       TCGA-BR-7958        TCGA-BR-7959        TCGA-BR-8059        TCGA-BR-8060 
"7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" 
       TCGA-BR-8077        TCGA-BR-8078        TCGA-BR-8080        TCGA-BR-8081 
"7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" 
       TCGA-BR-8284        TCGA-BR-8285        TCGA-BR-8286        TCGA-BR-8289 
"7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" 
       TCGA-BR-8291        TCGA-BR-8295        TCGA-BR-8296        TCGA-BR-8297 
"7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" 
       TCGA-BR-8592        TCGA-BR-A4IU        TCGA-BR-A4IV        TCGA-BR-A4IY 
"7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" 
       TCGA-BR-A4IZ        TCGA-BR-A4J1        TCGA-BR-A4J2        TCGA-BR-A4J4 
"7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" 
       TCGA-BR-A4J5        TCGA-BR-A4J6        TCGA-BR-A4J8        TCGA-BR-A4J9 
"7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" 
       TCGA-BR-A4PF        TCGA-BR-A4QI        TCGA-BR-A4QL        TCGA-CD-5798 
"7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" 
       TCGA-CD-5799        TCGA-CD-5800        TCGA-CD-5801        TCGA-CD-5802 
"7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" 
       TCGA-CD-5803        TCGA-CG-4300        TCGA-CG-4301        TCGA-CG-4304 
"7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" 
       TCGA-CG-4305        TCGA-CG-4306        TCGA-CG-4436        TCGA-CG-4437 
"7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" 
       TCGA-CG-4438        TCGA-CG-4440        TCGA-CG-4441        TCGA-CG-4443 
      "7Q LOSS CNV" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE"       "7Q LOSS CNV" 
       TCGA-CG-4444        TCGA-CG-4449        TCGA-CG-4455        TCGA-CG-4460 
"7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" 
       TCGA-CG-4462        TCGA-CG-4465        TCGA-CG-4466        TCGA-CG-4469 
"7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" 
       TCGA-CG-4472        TCGA-CG-4474        TCGA-CG-4477        TCGA-CG-5716 
"7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" 
       TCGA-CG-5717        TCGA-CG-5718        TCGA-CG-5719        TCGA-CG-5720 
"7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" 
       TCGA-CG-5721        TCGA-CG-5722        TCGA-CG-5723        TCGA-CG-5724 
"7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" 
       TCGA-CG-5725        TCGA-CG-5726        TCGA-CG-5727        TCGA-CG-5728 
"7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" 
       TCGA-CG-5730        TCGA-CG-5732        TCGA-CG-5733        TCGA-CG-5734 
"7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" 
       TCGA-D7-5577        TCGA-D7-5578        TCGA-D7-5579        TCGA-D7-6518 
"7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" 
       TCGA-D7-6519        TCGA-D7-6520        TCGA-D7-6521        TCGA-D7-6522 
"7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" 
       TCGA-D7-6524        TCGA-D7-6525        TCGA-D7-6526        TCGA-D7-6527 
"7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" 
       TCGA-D7-6528        TCGA-D7-6815        TCGA-D7-6817        TCGA-D7-6818 
"7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" 
       TCGA-D7-6820        TCGA-D7-6822        TCGA-EQ-5647        TCGA-EQ-8122 
      "7Q LOSS CNV" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" 
       TCGA-F1-6177        TCGA-F1-6874        TCGA-F1-6875        TCGA-FP-7735 
"7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" 
       TCGA-FP-7829        TCGA-FP-7916        TCGA-FP-7998        TCGA-FP-8099 
      "7Q LOSS CNV" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" 
       TCGA-FP-8209        TCGA-FP-8210        TCGA-FP-8631        TCGA-HJ-7597 
"7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE"       "7Q LOSS CNV" "7Q LOSS WILD-TYPE" 
       TCGA-IN-7806        TCGA-IN-7808        TCGA-IP-7968 
"7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" 
       TCGA-B7-5816        TCGA-B7-5818        TCGA-BR-6452        TCGA-BR-6455 
"7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" 
       TCGA-BR-6457        TCGA-BR-6458        TCGA-BR-6563        TCGA-BR-6564 
"7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" 
       TCGA-BR-6565        TCGA-BR-6566        TCGA-BR-6705        TCGA-BR-6706 
"7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" 
       TCGA-BR-6707        TCGA-BR-6709        TCGA-BR-6710        TCGA-BR-6801 
"7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" 
       TCGA-BR-6802        TCGA-BR-6803        TCGA-BR-6852        TCGA-BR-7196 
"7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" 
       TCGA-BR-7197        TCGA-BR-7703        TCGA-BR-7704        TCGA-BR-7707 
"7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" 
       TCGA-BR-7715        TCGA-BR-7716        TCGA-BR-7717        TCGA-BR-7722 
"7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" 
       TCGA-BR-7723        TCGA-BR-7851        TCGA-BR-7901        TCGA-BR-7957 
      "7Q LOSS CNV" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" 
       TCGA-BR-7958        TCGA-BR-7959        TCGA-BR-8059        TCGA-BR-8060 
"7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" 
       TCGA-BR-8077        TCGA-BR-8078        TCGA-BR-8080        TCGA-BR-8081 
"7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" 
       TCGA-BR-8284        TCGA-BR-8285        TCGA-BR-8286        TCGA-BR-8289 
"7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" 
       TCGA-BR-8291        TCGA-BR-8295        TCGA-BR-8296        TCGA-BR-8297 
"7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" 
       TCGA-BR-8592        TCGA-BR-A4IU        TCGA-BR-A4IV        TCGA-BR-A4IY 
"7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" 
       TCGA-BR-A4IZ        TCGA-BR-A4J1        TCGA-BR-A4J2        TCGA-BR-A4J4 
"7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" 
       TCGA-BR-A4J5        TCGA-BR-A4J6        TCGA-BR-A4J8        TCGA-BR-A4J9 
"7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" 
       TCGA-BR-A4PF        TCGA-BR-A4QI        TCGA-BR-A4QL        TCGA-CD-5798 
"7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" 
       TCGA-CD-5799        TCGA-CD-5800        TCGA-CD-5801        TCGA-CD-5802 
"7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" 
       TCGA-CD-5803        TCGA-CG-4300        TCGA-CG-4301        TCGA-CG-4304 
"7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" 
       TCGA-CG-4305        TCGA-CG-4306        TCGA-CG-4436        TCGA-CG-4437 
"7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" 
       TCGA-CG-4438        TCGA-CG-4440        TCGA-CG-4441        TCGA-CG-4443 
      "7Q LOSS CNV" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE"       "7Q LOSS CNV" 
       TCGA-CG-4444        TCGA-CG-4449        TCGA-CG-4455        TCGA-CG-4460 
"7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" 
       TCGA-CG-4462        TCGA-CG-4465        TCGA-CG-4466        TCGA-CG-4469 
"7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" 
       TCGA-CG-4472        TCGA-CG-4474        TCGA-CG-4477        TCGA-CG-5716 
"7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" 
       TCGA-CG-5717        TCGA-CG-5718        TCGA-CG-5719        TCGA-CG-5720 
"7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" 
       TCGA-CG-5721        TCGA-CG-5722        TCGA-CG-5723        TCGA-CG-5724 
"7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" 
       TCGA-CG-5725        TCGA-CG-5726        TCGA-CG-5727        TCGA-CG-5728 
"7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" 
       TCGA-CG-5730        TCGA-CG-5732        TCGA-CG-5733        TCGA-CG-5734 
"7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" 
       TCGA-D7-5577        TCGA-D7-5578        TCGA-D7-5579        TCGA-D7-6518 
"7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" 
       TCGA-D7-6519        TCGA-D7-6520        TCGA-D7-6521        TCGA-D7-6522 
"7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" 
       TCGA-D7-6524        TCGA-D7-6525        TCGA-D7-6526        TCGA-D7-6527 
"7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" 
       TCGA-D7-6528        TCGA-D7-6815        TCGA-D7-6817        TCGA-D7-6818 
"7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" 
       TCGA-D7-6820        TCGA-D7-6822        TCGA-EQ-5647        TCGA-EQ-8122 
      "7Q LOSS CNV" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" 
       TCGA-F1-6177        TCGA-F1-6874        TCGA-F1-6875        TCGA-FP-7735 
"7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" 
       TCGA-FP-7829        TCGA-FP-7916        TCGA-FP-7998        TCGA-FP-8099 
      "7Q LOSS CNV" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" 
       TCGA-FP-8209        TCGA-FP-8210        TCGA-FP-8631        TCGA-HJ-7597 
"7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE"       "7Q LOSS CNV" "7Q LOSS WILD-TYPE" 
       TCGA-IN-7806        TCGA-IN-7808        TCGA-IP-7968 
"7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" 
       TCGA-B7-5816        TCGA-B7-5818        TCGA-BR-6452        TCGA-BR-6455 
"7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" 
       TCGA-BR-6457        TCGA-BR-6458        TCGA-BR-6563        TCGA-BR-6564 
"7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" 
       TCGA-BR-6565        TCGA-BR-6566        TCGA-BR-6705        TCGA-BR-6706 
"7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" 
       TCGA-BR-6707        TCGA-BR-6709        TCGA-BR-6710        TCGA-BR-6801 
"7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" 
       TCGA-BR-6802        TCGA-BR-6803        TCGA-BR-6852        TCGA-BR-7196 
"7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" 
       TCGA-BR-7197        TCGA-BR-7703        TCGA-BR-7704        TCGA-BR-7707 
"7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" 
       TCGA-BR-7715        TCGA-BR-7716        TCGA-BR-7717        TCGA-BR-7722 
"7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" 
       TCGA-BR-7723        TCGA-BR-7851        TCGA-BR-7901        TCGA-BR-7957 
      "7Q LOSS CNV" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" 
       TCGA-BR-7958        TCGA-BR-7959        TCGA-BR-8059        TCGA-BR-8060 
"7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" 
       TCGA-BR-8077        TCGA-BR-8078        TCGA-BR-8080        TCGA-BR-8081 
"7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" 
       TCGA-BR-8284        TCGA-BR-8285        TCGA-BR-8286        TCGA-BR-8289 
"7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" 
       TCGA-BR-8291        TCGA-BR-8295        TCGA-BR-8296        TCGA-BR-8297 
"7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" 
       TCGA-BR-8592        TCGA-BR-A4IU        TCGA-BR-A4IV        TCGA-BR-A4IY 
"7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" 
       TCGA-BR-A4IZ        TCGA-BR-A4J1        TCGA-BR-A4J2        TCGA-BR-A4J4 
"7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" 
       TCGA-BR-A4J5        TCGA-BR-A4J6        TCGA-BR-A4J8        TCGA-BR-A4J9 
"7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" 
       TCGA-BR-A4PF        TCGA-BR-A4QI        TCGA-BR-A4QL        TCGA-CD-5798 
"7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" 
       TCGA-CD-5799        TCGA-CD-5800        TCGA-CD-5801        TCGA-CD-5802 
"7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" 
       TCGA-CD-5803        TCGA-CG-4300        TCGA-CG-4301        TCGA-CG-4304 
"7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" 
       TCGA-CG-4305        TCGA-CG-4306        TCGA-CG-4436        TCGA-CG-4437 
"7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" 
       TCGA-CG-4438        TCGA-CG-4440        TCGA-CG-4441        TCGA-CG-4443 
      "7Q LOSS CNV" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE"       "7Q LOSS CNV" 
       TCGA-CG-4444        TCGA-CG-4449        TCGA-CG-4455        TCGA-CG-4460 
"7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" 
       TCGA-CG-4462        TCGA-CG-4465        TCGA-CG-4466        TCGA-CG-4469 
"7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" 
       TCGA-CG-4472        TCGA-CG-4474        TCGA-CG-4477        TCGA-CG-5716 
"7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" 
       TCGA-CG-5717        TCGA-CG-5718        TCGA-CG-5719        TCGA-CG-5720 
"7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" 
       TCGA-CG-5721        TCGA-CG-5722        TCGA-CG-5723        TCGA-CG-5724 
"7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" 
       TCGA-CG-5725        TCGA-CG-5726        TCGA-CG-5727        TCGA-CG-5728 
"7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" 
       TCGA-CG-5730        TCGA-CG-5732        TCGA-CG-5733        TCGA-CG-5734 
"7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" 
       TCGA-D7-5577        TCGA-D7-5578        TCGA-D7-5579        TCGA-D7-6518 
"7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" 
       TCGA-D7-6519        TCGA-D7-6520        TCGA-D7-6521        TCGA-D7-6522 
"7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" 
       TCGA-D7-6524        TCGA-D7-6525        TCGA-D7-6526        TCGA-D7-6527 
"7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" 
       TCGA-D7-6528        TCGA-D7-6815        TCGA-D7-6817        TCGA-D7-6818 
"7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" 
       TCGA-D7-6820        TCGA-D7-6822        TCGA-EQ-5647        TCGA-EQ-8122 
      "7Q LOSS CNV" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" 
       TCGA-F1-6177        TCGA-F1-6874        TCGA-F1-6875        TCGA-FP-7735 
"7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" 
       TCGA-FP-7829        TCGA-FP-7916        TCGA-FP-7998        TCGA-FP-8099 
      "7Q LOSS CNV" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" 
       TCGA-FP-8209        TCGA-FP-8210        TCGA-FP-8631        TCGA-HJ-7597 
"7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE"       "7Q LOSS CNV" "7Q LOSS WILD-TYPE" 
       TCGA-IN-7806        TCGA-IN-7808        TCGA-IP-7968 
"7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" 
[1] "hr="     "7.9e+07"
D49V2, continuous
D49V3, binary
[1] "tbl2"
                   cls
clus                [,1] [,2]
  7Q LOSS CNV          0    6
  7Q LOSS WILD-TYPE   72  102
        clus
vv       7Q LOSS CNV 7Q LOSS WILD-TYPE
  FEMALE           0                72
  MALE             6               102
                   vv
clus                STOMACH  ADENOCARCINOMA  DIFFUSE TYPE
  7Q LOSS CNV                                           0
  7Q LOSS WILD-TYPE                                    10
                   vv
clus                STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  7Q LOSS CNV                                                            0
  7Q LOSS WILD-TYPE                                                     16
                   vv
clus                STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  7Q LOSS CNV                                                                       1
  7Q LOSS WILD-TYPE                                                                 7
                   vv
clus                STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE
  7Q LOSS CNV                                                              0
  7Q LOSS WILD-TYPE                                                        3
                   vv
clus                STOMACH ADENOCARCINOMA  SIGNET RING TYPE
  7Q LOSS CNV                                              0
  7Q LOSS WILD-TYPE                                        1
                   vv
clus                STOMACH ADENOCARCINOMA - DIFFUSE TYPE
  7Q LOSS CNV                                           0
  7Q LOSS WILD-TYPE                                    16
                   vv
clus                STOMACH ADENOCARCINOMA - NOT OTHERWISE SPECIFIED (NOS)
  7Q LOSS CNV                                                            1
  7Q LOSS WILD-TYPE                                                     72
                   vv
clus                STOMACH INTESTINAL ADENOCARCINOMA - MUCINOUS TYPE
  7Q LOSS CNV                                                       1
  7Q LOSS WILD-TYPE                                                 6
                   vv
clus                STOMACH INTESTINAL ADENOCARCINOMA - PAPILLARY TYPE
  7Q LOSS CNV                                                        0
  7Q LOSS WILD-TYPE                                                  3
                   vv
clus                STOMACH INTESTINAL ADENOCARCINOMA - TUBULAR TYPE
  7Q LOSS CNV                                                      1
  7Q LOSS WILD-TYPE                                                9
                   vv
clus                STOMACH INTESTINAL ADENOCARCINOMA - TYPE NOT OTHERWISE SPECIFIED (NOS)
  7Q LOSS CNV                                                                            2
  7Q LOSS WILD-TYPE                                                                     26
D49V4, multiclass
                   vv
clus                T1 T2 T3 T4
  7Q LOSS CNV        1  1  2  1
  7Q LOSS WILD-TYPE  5 51 54 17
D49V5, multiclass
    clus
vv   7Q LOSS CNV 7Q LOSS WILD-TYPE
  T1           1                 5
  T2           1                51
  T3           2                54
  T4           1                17
                   vv
clus                N0 N1 N2 N3
  7Q LOSS CNV        1  2  2  0
  7Q LOSS WILD-TYPE 43 47 21 15
D49V6, multiclass
    clus
vv   7Q LOSS CNV 7Q LOSS WILD-TYPE
  N0           1                43
  N1           2                47
  N2           2                21
  N3           0                15
                   vv
clus                 M0  M1  MX
  7Q LOSS CNV         5   0   0
  7Q LOSS WILD-TYPE 113  16   8
D49V7, multiclass
    clus
vv   7Q LOSS CNV 7Q LOSS WILD-TYPE
  M0           5               113
  M1           0                16
  MX           0                 8
                   vv
clus                 I II III IV
  7Q LOSS CNV        1  2   1  1
  7Q LOSS WILD-TYPE 23 35  38 25
D49V8, multiclass
     clus
vv    7Q LOSS CNV 7Q LOSS WILD-TYPE
  I             1                23
  II            2                35
  III           1                38
  IV            1                25
D49V9, binary
[1] "tbl2"
                   cls
clus                [,1] [,2]
  7Q LOSS CNV          0    6
  7Q LOSS WILD-TYPE    5  169
     clus
vv    7Q LOSS CNV 7Q LOSS WILD-TYPE
  NO            0                 5
  YES           6               169
                   vv
clus                 R0  R1  R2  RX
  7Q LOSS CNV         6   0   0   0
  7Q LOSS WILD-TYPE 119   7  12  25
D49V10, multiclass
    clus
vv   7Q LOSS CNV 7Q LOSS WILD-TYPE
  R0           6               119
  R1           0                 7
  R2           0                12
  RX           0                25
D49V11, continuous

Clustering(50) Variable = 8p loss
D50V1, survival
                   sevent
clus2                 0   1
  8P LOSS CNV        15   1
  8P LOSS WILD-TYPE 109  18
      8P LOSS CNV 8P LOSS WILD-TYPE 
               16               127 
      8P LOSS CNV 8P LOSS WILD-TYPE 
                1                18 
$`8P LOSS CNV`
TCGA-BR-7716 TCGA-BR-8077 TCGA-BR-8286 TCGA-BR-A4IY TCGA-BR-A4J1 TCGA-BR-A4PF 
        0.82         0.69         0.43         0.39         0.72         0.72 
TCGA-BR-A4QI TCGA-CG-4301 TCGA-CG-4436 TCGA-CG-4449 TCGA-CG-5730 TCGA-D7-6528 
        0.49         3.02        52.96        19.07         4.01         1.68 
TCGA-D7-6820 TCGA-F1-6177 TCGA-FP-8099 TCGA-IP-7968 
        2.93         6.54         1.02         2.53 

$`8P LOSS WILD-TYPE`
TCGA-B7-5816 TCGA-B7-5818 TCGA-BR-6452 TCGA-BR-6455 TCGA-BR-6457 TCGA-BR-6458 
        5.62         0.10         0.95         1.41         1.35         1.35 
TCGA-BR-6563 TCGA-BR-6564 TCGA-BR-6565 TCGA-BR-6566 TCGA-BR-6705 TCGA-BR-6706 
        0.85         0.82         0.62         0.62         1.71         2.17 
TCGA-BR-6707 TCGA-BR-6709 TCGA-BR-6710 TCGA-BR-6801 TCGA-BR-6802 TCGA-BR-6803 
        0.99         1.22         0.66         1.12         0.76         0.66 
TCGA-BR-6852 TCGA-BR-7196 TCGA-BR-7197 TCGA-BR-7703 TCGA-BR-7704 TCGA-BR-7707 
        0.26         1.22         1.48         0.46         1.25         0.13 
TCGA-BR-7715 TCGA-BR-7717 TCGA-BR-7722 TCGA-BR-7723 TCGA-BR-7851 TCGA-BR-7901 
        1.05         0.69         0.16         4.54         0.99         0.95 
TCGA-BR-7957 TCGA-BR-7958 TCGA-BR-7959 TCGA-BR-8059 TCGA-BR-8060 TCGA-BR-8078 
        0.69         0.16         1.08         0.82         1.32         0.95 
TCGA-BR-8080 TCGA-BR-8081 TCGA-BR-8284 TCGA-BR-8285 TCGA-BR-8289 TCGA-BR-8291 
        0.49         0.46         0.72         0.26         0.26         1.18 
TCGA-BR-8295 TCGA-BR-8296 TCGA-BR-8297 TCGA-BR-8592 TCGA-BR-A4IU TCGA-BR-A4IV 
        1.55         1.48         0.76         0.20         0.59         0.92 
TCGA-BR-A4IZ TCGA-BR-A4J2 TCGA-BR-A4J4 TCGA-BR-A4J5 TCGA-BR-A4J6 TCGA-BR-A4J8 
        0.79         0.79         0.53         0.43         0.13         0.23 
TCGA-BR-A4J9 TCGA-BR-A4QL TCGA-CD-5798 TCGA-CD-5799 TCGA-CD-5800 TCGA-CD-5801 
        0.10         2.24         0.82         0.69         0.36         0.49 
TCGA-CD-5802 TCGA-CD-5803 TCGA-CG-4300 TCGA-CG-4304 TCGA-CG-4305 TCGA-CG-4306 
        0.30         0.07        20.02        27.02        15.95         1.02 
TCGA-CG-4437 TCGA-CG-4438 TCGA-CG-4440 TCGA-CG-4441 TCGA-CG-4443 TCGA-CG-4444 
        8.05        54.05         4.01        14.01        29.98        47.05 
TCGA-CG-4455 TCGA-CG-4460 TCGA-CG-4462 TCGA-CG-4465 TCGA-CG-4466 TCGA-CG-4469 
       12.03        21.99         1.02         8.98        18.94         7.07 
TCGA-CG-4472 TCGA-CG-4474 TCGA-CG-4477 TCGA-CG-5716 TCGA-CG-5717 TCGA-CG-5718 
       12.00         1.02         1.02         1.02         6.94         1.02 
TCGA-CG-5719 TCGA-CG-5720 TCGA-CG-5721 TCGA-CG-5722 TCGA-CG-5723 TCGA-CG-5724 
        1.02         0.99         5.98         0.95        70.06        12.03 
TCGA-CG-5725 TCGA-CG-5726 TCGA-CG-5727 TCGA-CG-5728 TCGA-CG-5732 TCGA-CG-5733 
       15.02        28.96        31.04        65.10        55.04        21.07 
TCGA-CG-5734 TCGA-D7-5577 TCGA-D7-5578 TCGA-D7-5579 TCGA-D7-6518 TCGA-D7-6519 
        7.99         8.65         3.58         4.54         9.80        15.65 
TCGA-D7-6520 TCGA-D7-6521 TCGA-D7-6522 TCGA-D7-6524 TCGA-D7-6525 TCGA-D7-6526 
        9.63         8.19         6.90         0.69         5.95         6.61 
TCGA-D7-6527 TCGA-D7-6815 TCGA-D7-6817 TCGA-D7-6818 TCGA-D7-6822 TCGA-EQ-5647 
        4.14         3.65         4.70         4.04         4.27         0.62 
TCGA-EQ-8122 TCGA-F1-6874 TCGA-F1-6875 TCGA-FP-7735 TCGA-FP-7829 TCGA-FP-7916 
        7.79         2.01        72.23         0.39         0.20         3.02 
TCGA-FP-7998 TCGA-FP-8209 TCGA-FP-8210 TCGA-FP-8631 TCGA-HJ-7597 TCGA-IN-7806 
        3.58        59.05         5.03         0.56        26.43         6.87 
TCGA-IN-7808 
        3.55 

      8P LOSS CNV 8P LOSS WILD-TYPE 
             0.39              0.07 
      8P LOSS CNV 8P LOSS WILD-TYPE 
            52.96             72.23 
      8P LOSS CNV 8P LOSS WILD-TYPE 
             1.35              1.25 
[1] "0.4 - 53.0 (1.4)" "0.1 - 72.2 (1.2)"
       TCGA-B7-5816        TCGA-B7-5818        TCGA-BR-6452        TCGA-BR-6455 
"8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" 
       TCGA-BR-6457        TCGA-BR-6458        TCGA-BR-6563        TCGA-BR-6564 
"8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" 
       TCGA-BR-6565        TCGA-BR-6566        TCGA-BR-6705        TCGA-BR-6706 
"8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" 
       TCGA-BR-6707        TCGA-BR-6709        TCGA-BR-6710        TCGA-BR-6801 
"8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" 
       TCGA-BR-6802        TCGA-BR-6803        TCGA-BR-6852        TCGA-BR-7196 
"8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" 
       TCGA-BR-7197        TCGA-BR-7703        TCGA-BR-7704        TCGA-BR-7707 
"8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" 
       TCGA-BR-7715        TCGA-BR-7716        TCGA-BR-7717        TCGA-BR-7722 
"8P LOSS WILD-TYPE"       "8P LOSS CNV" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" 
       TCGA-BR-7723        TCGA-BR-7851        TCGA-BR-7901        TCGA-BR-7957 
"8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" 
       TCGA-BR-7958        TCGA-BR-7959        TCGA-BR-8059        TCGA-BR-8060 
"8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" 
       TCGA-BR-8077        TCGA-BR-8078        TCGA-BR-8080        TCGA-BR-8081 
      "8P LOSS CNV" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" 
       TCGA-BR-8284        TCGA-BR-8285        TCGA-BR-8286        TCGA-BR-8289 
"8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE"       "8P LOSS CNV" "8P LOSS WILD-TYPE" 
       TCGA-BR-8291        TCGA-BR-8295        TCGA-BR-8296        TCGA-BR-8297 
"8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" 
       TCGA-BR-8592        TCGA-BR-A4IU        TCGA-BR-A4IV        TCGA-BR-A4IY 
"8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE"       "8P LOSS CNV" 
       TCGA-BR-A4IZ        TCGA-BR-A4J1        TCGA-BR-A4J2        TCGA-BR-A4J4 
"8P LOSS WILD-TYPE"       "8P LOSS CNV" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" 
       TCGA-BR-A4J5        TCGA-BR-A4J6        TCGA-BR-A4J8        TCGA-BR-A4J9 
"8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" 
       TCGA-BR-A4PF        TCGA-BR-A4QI        TCGA-BR-A4QL        TCGA-CD-5798 
      "8P LOSS CNV"       "8P LOSS CNV" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" 
       TCGA-CD-5799        TCGA-CD-5800        TCGA-CD-5801        TCGA-CD-5802 
"8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" 
       TCGA-CD-5803        TCGA-CG-4300        TCGA-CG-4301        TCGA-CG-4304 
"8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE"       "8P LOSS CNV" "8P LOSS WILD-TYPE" 
       TCGA-CG-4305        TCGA-CG-4306        TCGA-CG-4436        TCGA-CG-4437 
"8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE"       "8P LOSS CNV" "8P LOSS WILD-TYPE" 
       TCGA-CG-4438        TCGA-CG-4440        TCGA-CG-4441        TCGA-CG-4443 
"8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" 
       TCGA-CG-4444        TCGA-CG-4449        TCGA-CG-4455        TCGA-CG-4460 
"8P LOSS WILD-TYPE"       "8P LOSS CNV" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" 
       TCGA-CG-4462        TCGA-CG-4465        TCGA-CG-4466        TCGA-CG-4469 
"8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" 
       TCGA-CG-4472        TCGA-CG-4474        TCGA-CG-4477        TCGA-CG-5716 
"8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" 
       TCGA-CG-5717        TCGA-CG-5718        TCGA-CG-5719        TCGA-CG-5720 
"8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" 
       TCGA-CG-5721        TCGA-CG-5722        TCGA-CG-5723        TCGA-CG-5724 
"8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" 
       TCGA-CG-5725        TCGA-CG-5726        TCGA-CG-5727        TCGA-CG-5728 
"8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" 
       TCGA-CG-5730        TCGA-CG-5732        TCGA-CG-5733        TCGA-CG-5734 
      "8P LOSS CNV" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" 
       TCGA-D7-5577        TCGA-D7-5578        TCGA-D7-5579        TCGA-D7-6518 
"8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" 
       TCGA-D7-6519        TCGA-D7-6520        TCGA-D7-6521        TCGA-D7-6522 
"8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" 
       TCGA-D7-6524        TCGA-D7-6525        TCGA-D7-6526        TCGA-D7-6527 
"8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" 
       TCGA-D7-6528        TCGA-D7-6815        TCGA-D7-6817        TCGA-D7-6818 
      "8P LOSS CNV" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" 
       TCGA-D7-6820        TCGA-D7-6822        TCGA-EQ-5647        TCGA-EQ-8122 
      "8P LOSS CNV" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" 
       TCGA-F1-6177        TCGA-F1-6874        TCGA-F1-6875        TCGA-FP-7735 
      "8P LOSS CNV" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" 
       TCGA-FP-7829        TCGA-FP-7916        TCGA-FP-7998        TCGA-FP-8099 
"8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE"       "8P LOSS CNV" 
       TCGA-FP-8209        TCGA-FP-8210        TCGA-FP-8631        TCGA-HJ-7597 
"8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" 
       TCGA-IN-7806        TCGA-IN-7808        TCGA-IP-7968 
"8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE"       "8P LOSS CNV" 
       TCGA-B7-5816        TCGA-B7-5818        TCGA-BR-6452        TCGA-BR-6455 
"8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" 
       TCGA-BR-6457        TCGA-BR-6458        TCGA-BR-6563        TCGA-BR-6564 
"8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" 
       TCGA-BR-6565        TCGA-BR-6566        TCGA-BR-6705        TCGA-BR-6706 
"8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" 
       TCGA-BR-6707        TCGA-BR-6709        TCGA-BR-6710        TCGA-BR-6801 
"8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" 
       TCGA-BR-6802        TCGA-BR-6803        TCGA-BR-6852        TCGA-BR-7196 
"8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" 
       TCGA-BR-7197        TCGA-BR-7703        TCGA-BR-7704        TCGA-BR-7707 
"8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" 
       TCGA-BR-7715        TCGA-BR-7716        TCGA-BR-7717        TCGA-BR-7722 
"8P LOSS WILD-TYPE"       "8P LOSS CNV" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" 
       TCGA-BR-7723        TCGA-BR-7851        TCGA-BR-7901        TCGA-BR-7957 
"8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" 
       TCGA-BR-7958        TCGA-BR-7959        TCGA-BR-8059        TCGA-BR-8060 
"8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" 
       TCGA-BR-8077        TCGA-BR-8078        TCGA-BR-8080        TCGA-BR-8081 
      "8P LOSS CNV" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" 
       TCGA-BR-8284        TCGA-BR-8285        TCGA-BR-8286        TCGA-BR-8289 
"8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE"       "8P LOSS CNV" "8P LOSS WILD-TYPE" 
       TCGA-BR-8291        TCGA-BR-8295        TCGA-BR-8296        TCGA-BR-8297 
"8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" 
       TCGA-BR-8592        TCGA-BR-A4IU        TCGA-BR-A4IV        TCGA-BR-A4IY 
"8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE"       "8P LOSS CNV" 
       TCGA-BR-A4IZ        TCGA-BR-A4J1        TCGA-BR-A4J2        TCGA-BR-A4J4 
"8P LOSS WILD-TYPE"       "8P LOSS CNV" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" 
       TCGA-BR-A4J5        TCGA-BR-A4J6        TCGA-BR-A4J8        TCGA-BR-A4J9 
"8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" 
       TCGA-BR-A4PF        TCGA-BR-A4QI        TCGA-BR-A4QL        TCGA-CD-5798 
      "8P LOSS CNV"       "8P LOSS CNV" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" 
       TCGA-CD-5799        TCGA-CD-5800        TCGA-CD-5801        TCGA-CD-5802 
"8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" 
       TCGA-CD-5803        TCGA-CG-4300        TCGA-CG-4301        TCGA-CG-4304 
"8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE"       "8P LOSS CNV" "8P LOSS WILD-TYPE" 
       TCGA-CG-4305        TCGA-CG-4306        TCGA-CG-4436        TCGA-CG-4437 
"8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE"       "8P LOSS CNV" "8P LOSS WILD-TYPE" 
       TCGA-CG-4438        TCGA-CG-4440        TCGA-CG-4441        TCGA-CG-4443 
"8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" 
       TCGA-CG-4444        TCGA-CG-4449        TCGA-CG-4455        TCGA-CG-4460 
"8P LOSS WILD-TYPE"       "8P LOSS CNV" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" 
       TCGA-CG-4462        TCGA-CG-4465        TCGA-CG-4466        TCGA-CG-4469 
"8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" 
       TCGA-CG-4472        TCGA-CG-4474        TCGA-CG-4477        TCGA-CG-5716 
"8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" 
       TCGA-CG-5717        TCGA-CG-5718        TCGA-CG-5719        TCGA-CG-5720 
"8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" 
       TCGA-CG-5721        TCGA-CG-5722        TCGA-CG-5723        TCGA-CG-5724 
"8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" 
       TCGA-CG-5725        TCGA-CG-5726        TCGA-CG-5727        TCGA-CG-5728 
"8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" 
       TCGA-CG-5730        TCGA-CG-5732        TCGA-CG-5733        TCGA-CG-5734 
      "8P LOSS CNV" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" 
       TCGA-D7-5577        TCGA-D7-5578        TCGA-D7-5579        TCGA-D7-6518 
"8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" 
       TCGA-D7-6519        TCGA-D7-6520        TCGA-D7-6521        TCGA-D7-6522 
"8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" 
       TCGA-D7-6524        TCGA-D7-6525        TCGA-D7-6526        TCGA-D7-6527 
"8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" 
       TCGA-D7-6528        TCGA-D7-6815        TCGA-D7-6817        TCGA-D7-6818 
      "8P LOSS CNV" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" 
       TCGA-D7-6820        TCGA-D7-6822        TCGA-EQ-5647        TCGA-EQ-8122 
      "8P LOSS CNV" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" 
       TCGA-F1-6177        TCGA-F1-6874        TCGA-F1-6875        TCGA-FP-7735 
      "8P LOSS CNV" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" 
       TCGA-FP-7829        TCGA-FP-7916        TCGA-FP-7998        TCGA-FP-8099 
"8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE"       "8P LOSS CNV" 
       TCGA-FP-8209        TCGA-FP-8210        TCGA-FP-8631        TCGA-HJ-7597 
"8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" 
       TCGA-IN-7806        TCGA-IN-7808        TCGA-IP-7968 
"8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE"       "8P LOSS CNV" 
       TCGA-B7-5816        TCGA-B7-5818        TCGA-BR-6452        TCGA-BR-6455 
"8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" 
       TCGA-BR-6457        TCGA-BR-6458        TCGA-BR-6563        TCGA-BR-6564 
"8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" 
       TCGA-BR-6565        TCGA-BR-6566        TCGA-BR-6705        TCGA-BR-6706 
"8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" 
       TCGA-BR-6707        TCGA-BR-6709        TCGA-BR-6710        TCGA-BR-6801 
"8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" 
       TCGA-BR-6802        TCGA-BR-6803        TCGA-BR-6852        TCGA-BR-7196 
"8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" 
       TCGA-BR-7197        TCGA-BR-7703        TCGA-BR-7704        TCGA-BR-7707 
"8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" 
       TCGA-BR-7715        TCGA-BR-7716        TCGA-BR-7717        TCGA-BR-7722 
"8P LOSS WILD-TYPE"       "8P LOSS CNV" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" 
       TCGA-BR-7723        TCGA-BR-7851        TCGA-BR-7901        TCGA-BR-7957 
"8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" 
       TCGA-BR-7958        TCGA-BR-7959        TCGA-BR-8059        TCGA-BR-8060 
"8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" 
       TCGA-BR-8077        TCGA-BR-8078        TCGA-BR-8080        TCGA-BR-8081 
      "8P LOSS CNV" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" 
       TCGA-BR-8284        TCGA-BR-8285        TCGA-BR-8286        TCGA-BR-8289 
"8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE"       "8P LOSS CNV" "8P LOSS WILD-TYPE" 
       TCGA-BR-8291        TCGA-BR-8295        TCGA-BR-8296        TCGA-BR-8297 
"8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" 
       TCGA-BR-8592        TCGA-BR-A4IU        TCGA-BR-A4IV        TCGA-BR-A4IY 
"8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE"       "8P LOSS CNV" 
       TCGA-BR-A4IZ        TCGA-BR-A4J1        TCGA-BR-A4J2        TCGA-BR-A4J4 
"8P LOSS WILD-TYPE"       "8P LOSS CNV" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" 
       TCGA-BR-A4J5        TCGA-BR-A4J6        TCGA-BR-A4J8        TCGA-BR-A4J9 
"8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" 
       TCGA-BR-A4PF        TCGA-BR-A4QI        TCGA-BR-A4QL        TCGA-CD-5798 
      "8P LOSS CNV"       "8P LOSS CNV" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" 
       TCGA-CD-5799        TCGA-CD-5800        TCGA-CD-5801        TCGA-CD-5802 
"8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" 
       TCGA-CD-5803        TCGA-CG-4300        TCGA-CG-4301        TCGA-CG-4304 
"8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE"       "8P LOSS CNV" "8P LOSS WILD-TYPE" 
       TCGA-CG-4305        TCGA-CG-4306        TCGA-CG-4436        TCGA-CG-4437 
"8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE"       "8P LOSS CNV" "8P LOSS WILD-TYPE" 
       TCGA-CG-4438        TCGA-CG-4440        TCGA-CG-4441        TCGA-CG-4443 
"8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" 
       TCGA-CG-4444        TCGA-CG-4449        TCGA-CG-4455        TCGA-CG-4460 
"8P LOSS WILD-TYPE"       "8P LOSS CNV" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" 
       TCGA-CG-4462        TCGA-CG-4465        TCGA-CG-4466        TCGA-CG-4469 
"8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" 
       TCGA-CG-4472        TCGA-CG-4474        TCGA-CG-4477        TCGA-CG-5716 
"8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" 
       TCGA-CG-5717        TCGA-CG-5718        TCGA-CG-5719        TCGA-CG-5720 
"8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" 
       TCGA-CG-5721        TCGA-CG-5722        TCGA-CG-5723        TCGA-CG-5724 
"8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" 
       TCGA-CG-5725        TCGA-CG-5726        TCGA-CG-5727        TCGA-CG-5728 
"8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" 
       TCGA-CG-5730        TCGA-CG-5732        TCGA-CG-5733        TCGA-CG-5734 
      "8P LOSS CNV" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" 
       TCGA-D7-5577        TCGA-D7-5578        TCGA-D7-5579        TCGA-D7-6518 
"8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" 
       TCGA-D7-6519        TCGA-D7-6520        TCGA-D7-6521        TCGA-D7-6522 
"8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" 
       TCGA-D7-6524        TCGA-D7-6525        TCGA-D7-6526        TCGA-D7-6527 
"8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" 
       TCGA-D7-6528        TCGA-D7-6815        TCGA-D7-6817        TCGA-D7-6818 
      "8P LOSS CNV" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" 
       TCGA-D7-6820        TCGA-D7-6822        TCGA-EQ-5647        TCGA-EQ-8122 
      "8P LOSS CNV" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" 
       TCGA-F1-6177        TCGA-F1-6874        TCGA-F1-6875        TCGA-FP-7735 
      "8P LOSS CNV" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" 
       TCGA-FP-7829        TCGA-FP-7916        TCGA-FP-7998        TCGA-FP-8099 
"8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE"       "8P LOSS CNV" 
       TCGA-FP-8209        TCGA-FP-8210        TCGA-FP-8631        TCGA-HJ-7597 
"8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" 
       TCGA-IN-7806        TCGA-IN-7808        TCGA-IP-7968 
"8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE"       "8P LOSS CNV" 
[1] "hr=" "1.4"
D50V2, continuous
D50V3, binary
[1] "tbl2"
                   cls
clus                [,1] [,2]
  8P LOSS CNV          6   13
  8P LOSS WILD-TYPE   66   95
        clus
vv       8P LOSS CNV 8P LOSS WILD-TYPE
  FEMALE           6                66
  MALE            13                95
                   vv
clus                STOMACH  ADENOCARCINOMA  DIFFUSE TYPE
  8P LOSS CNV                                           0
  8P LOSS WILD-TYPE                                    10
                   vv
clus                STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  8P LOSS CNV                                                            6
  8P LOSS WILD-TYPE                                                     10
                   vv
clus                STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  8P LOSS CNV                                                                       1
  8P LOSS WILD-TYPE                                                                 7
                   vv
clus                STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE
  8P LOSS CNV                                                              0
  8P LOSS WILD-TYPE                                                        3
                   vv
clus                STOMACH ADENOCARCINOMA  SIGNET RING TYPE
  8P LOSS CNV                                              0
  8P LOSS WILD-TYPE                                        1
                   vv
clus                STOMACH ADENOCARCINOMA - DIFFUSE TYPE
  8P LOSS CNV                                           0
  8P LOSS WILD-TYPE                                    16
                   vv
clus                STOMACH ADENOCARCINOMA - NOT OTHERWISE SPECIFIED (NOS)
  8P LOSS CNV                                                            5
  8P LOSS WILD-TYPE                                                     68
                   vv
clus                STOMACH INTESTINAL ADENOCARCINOMA - MUCINOUS TYPE
  8P LOSS CNV                                                       1
  8P LOSS WILD-TYPE                                                 6
                   vv
clus                STOMACH INTESTINAL ADENOCARCINOMA - PAPILLARY TYPE
  8P LOSS CNV                                                        0
  8P LOSS WILD-TYPE                                                  3
                   vv
clus                STOMACH INTESTINAL ADENOCARCINOMA - TUBULAR TYPE
  8P LOSS CNV                                                      3
  8P LOSS WILD-TYPE                                                7
                   vv
clus                STOMACH INTESTINAL ADENOCARCINOMA - TYPE NOT OTHERWISE SPECIFIED (NOS)
  8P LOSS CNV                                                                            2
  8P LOSS WILD-TYPE                                                                     26
D50V4, multiclass
                   vv
clus                T1 T2 T3 T4
  8P LOSS CNV        1  6  2  2
  8P LOSS WILD-TYPE  5 46 54 16
D50V5, multiclass
    clus
vv   8P LOSS CNV 8P LOSS WILD-TYPE
  T1           1                 5
  T2           6                46
  T3           2                54
  T4           2                16
                   vv
clus                N0 N1 N2 N3
  8P LOSS CNV        2  8  1  0
  8P LOSS WILD-TYPE 42 41 22 15
D50V6, multiclass
    clus
vv   8P LOSS CNV 8P LOSS WILD-TYPE
  N0           2                42
  N1           8                41
  N2           1                22
  N3           0                15
                   vv
clus                 M0  M1  MX
  8P LOSS CNV         8   2   2
  8P LOSS WILD-TYPE 110  14   6
D50V7, multiclass
    clus
vv   8P LOSS CNV 8P LOSS WILD-TYPE
  M0           8               110
  M1           2                14
  MX           2                 6
                   vv
clus                 I II III IV
  8P LOSS CNV        3  3   1  3
  8P LOSS WILD-TYPE 21 34  38 23
D50V8, multiclass
     clus
vv    8P LOSS CNV 8P LOSS WILD-TYPE
  I             3                21
  II            3                34
  III           1                38
  IV            3                23
D50V9, binary
[1] "tbl2"
                   cls
clus                [,1] [,2]
  8P LOSS CNV          0   19
  8P LOSS WILD-TYPE    5  156
     clus
vv    8P LOSS CNV 8P LOSS WILD-TYPE
  NO            0                 5
  YES          19               156
                   vv
clus                 R0  R1  R2  RX
  8P LOSS CNV        14   0   2   2
  8P LOSS WILD-TYPE 111   7  10  23
D50V10, multiclass
    clus
vv   8P LOSS CNV 8P LOSS WILD-TYPE
  R0          14               111
  R1           0                 7
  R2           2                10
  RX           2                23
D50V11, continuous

Clustering(51) Variable = 8q loss
D51V1, survival
                   sevent
clus2                 0   1
  8Q LOSS CNV         4   0
  8Q LOSS WILD-TYPE 120  19
      8Q LOSS CNV 8Q LOSS WILD-TYPE 
                4               139 
      8Q LOSS CNV 8Q LOSS WILD-TYPE 
                0                19 
$`8Q LOSS CNV`
TCGA-BR-8286 TCGA-BR-A4QI TCGA-D7-6528 TCGA-FP-8099 
        0.43         0.49         1.68         1.02 

$`8Q LOSS WILD-TYPE`
TCGA-B7-5816 TCGA-B7-5818 TCGA-BR-6452 TCGA-BR-6455 TCGA-BR-6457 TCGA-BR-6458 
        5.62         0.10         0.95         1.41         1.35         1.35 
TCGA-BR-6563 TCGA-BR-6564 TCGA-BR-6565 TCGA-BR-6566 TCGA-BR-6705 TCGA-BR-6706 
        0.85         0.82         0.62         0.62         1.71         2.17 
TCGA-BR-6707 TCGA-BR-6709 TCGA-BR-6710 TCGA-BR-6801 TCGA-BR-6802 TCGA-BR-6803 
        0.99         1.22         0.66         1.12         0.76         0.66 
TCGA-BR-6852 TCGA-BR-7196 TCGA-BR-7197 TCGA-BR-7703 TCGA-BR-7704 TCGA-BR-7707 
        0.26         1.22         1.48         0.46         1.25         0.13 
TCGA-BR-7715 TCGA-BR-7716 TCGA-BR-7717 TCGA-BR-7722 TCGA-BR-7723 TCGA-BR-7851 
        1.05         0.82         0.69         0.16         4.54         0.99 
TCGA-BR-7901 TCGA-BR-7957 TCGA-BR-7958 TCGA-BR-7959 TCGA-BR-8059 TCGA-BR-8060 
        0.95         0.69         0.16         1.08         0.82         1.32 
TCGA-BR-8077 TCGA-BR-8078 TCGA-BR-8080 TCGA-BR-8081 TCGA-BR-8284 TCGA-BR-8285 
        0.69         0.95         0.49         0.46         0.72         0.26 
TCGA-BR-8289 TCGA-BR-8291 TCGA-BR-8295 TCGA-BR-8296 TCGA-BR-8297 TCGA-BR-8592 
        0.26         1.18         1.55         1.48         0.76         0.20 
TCGA-BR-A4IU TCGA-BR-A4IV TCGA-BR-A4IY TCGA-BR-A4IZ TCGA-BR-A4J1 TCGA-BR-A4J2 
        0.59         0.92         0.39         0.79         0.72         0.79 
TCGA-BR-A4J4 TCGA-BR-A4J5 TCGA-BR-A4J6 TCGA-BR-A4J8 TCGA-BR-A4J9 TCGA-BR-A4PF 
        0.53         0.43         0.13         0.23         0.10         0.72 
TCGA-BR-A4QL TCGA-CD-5798 TCGA-CD-5799 TCGA-CD-5800 TCGA-CD-5801 TCGA-CD-5802 
        2.24         0.82         0.69         0.36         0.49         0.30 
TCGA-CD-5803 TCGA-CG-4300 TCGA-CG-4301 TCGA-CG-4304 TCGA-CG-4305 TCGA-CG-4306 
        0.07        20.02         3.02        27.02        15.95         1.02 
TCGA-CG-4436 TCGA-CG-4437 TCGA-CG-4438 TCGA-CG-4440 TCGA-CG-4441 TCGA-CG-4443 
       52.96         8.05        54.05         4.01        14.01        29.98 
TCGA-CG-4444 TCGA-CG-4449 TCGA-CG-4455 TCGA-CG-4460 TCGA-CG-4462 TCGA-CG-4465 
       47.05        19.07        12.03        21.99         1.02         8.98 
TCGA-CG-4466 TCGA-CG-4469 TCGA-CG-4472 TCGA-CG-4474 TCGA-CG-4477 TCGA-CG-5716 
       18.94         7.07        12.00         1.02         1.02         1.02 
TCGA-CG-5717 TCGA-CG-5718 TCGA-CG-5719 TCGA-CG-5720 TCGA-CG-5721 TCGA-CG-5722 
        6.94         1.02         1.02         0.99         5.98         0.95 
TCGA-CG-5723 TCGA-CG-5724 TCGA-CG-5725 TCGA-CG-5726 TCGA-CG-5727 TCGA-CG-5728 
       70.06        12.03        15.02        28.96        31.04        65.10 
TCGA-CG-5730 TCGA-CG-5732 TCGA-CG-5733 TCGA-CG-5734 TCGA-D7-5577 TCGA-D7-5578 
        4.01        55.04        21.07         7.99         8.65         3.58 
TCGA-D7-5579 TCGA-D7-6518 TCGA-D7-6519 TCGA-D7-6520 TCGA-D7-6521 TCGA-D7-6522 
        4.54         9.80        15.65         9.63         8.19         6.90 
TCGA-D7-6524 TCGA-D7-6525 TCGA-D7-6526 TCGA-D7-6527 TCGA-D7-6815 TCGA-D7-6817 
        0.69         5.95         6.61         4.14         3.65         4.70 
TCGA-D7-6818 TCGA-D7-6820 TCGA-D7-6822 TCGA-EQ-5647 TCGA-EQ-8122 TCGA-F1-6177 
        4.04         2.93         4.27         0.62         7.79         6.54 
TCGA-F1-6874 TCGA-F1-6875 TCGA-FP-7735 TCGA-FP-7829 TCGA-FP-7916 TCGA-FP-7998 
        2.01        72.23         0.39         0.20         3.02         3.58 
TCGA-FP-8209 TCGA-FP-8210 TCGA-FP-8631 TCGA-HJ-7597 TCGA-IN-7806 TCGA-IN-7808 
       59.05         5.03         0.56        26.43         6.87         3.55 
TCGA-IP-7968 
        2.53 

      8Q LOSS CNV 8Q LOSS WILD-TYPE 
             0.43              0.07 
      8Q LOSS CNV 8Q LOSS WILD-TYPE 
             1.68             72.23 
      8Q LOSS CNV 8Q LOSS WILD-TYPE 
            0.755             1.320 
[1] "0.4 - 1.7 (0.8)"  "0.1 - 72.2 (1.3)"
       TCGA-B7-5816        TCGA-B7-5818        TCGA-BR-6452        TCGA-BR-6455 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-BR-6457        TCGA-BR-6458        TCGA-BR-6563        TCGA-BR-6564 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-BR-6565        TCGA-BR-6566        TCGA-BR-6705        TCGA-BR-6706 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-BR-6707        TCGA-BR-6709        TCGA-BR-6710        TCGA-BR-6801 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-BR-6802        TCGA-BR-6803        TCGA-BR-6852        TCGA-BR-7196 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-BR-7197        TCGA-BR-7703        TCGA-BR-7704        TCGA-BR-7707 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-BR-7715        TCGA-BR-7716        TCGA-BR-7717        TCGA-BR-7722 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-BR-7723        TCGA-BR-7851        TCGA-BR-7901        TCGA-BR-7957 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-BR-7958        TCGA-BR-7959        TCGA-BR-8059        TCGA-BR-8060 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-BR-8077        TCGA-BR-8078        TCGA-BR-8080        TCGA-BR-8081 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-BR-8284        TCGA-BR-8285        TCGA-BR-8286        TCGA-BR-8289 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE"       "8Q LOSS CNV" "8Q LOSS WILD-TYPE" 
       TCGA-BR-8291        TCGA-BR-8295        TCGA-BR-8296        TCGA-BR-8297 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-BR-8592        TCGA-BR-A4IU        TCGA-BR-A4IV        TCGA-BR-A4IY 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-BR-A4IZ        TCGA-BR-A4J1        TCGA-BR-A4J2        TCGA-BR-A4J4 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-BR-A4J5        TCGA-BR-A4J6        TCGA-BR-A4J8        TCGA-BR-A4J9 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-BR-A4PF        TCGA-BR-A4QI        TCGA-BR-A4QL        TCGA-CD-5798 
"8Q LOSS WILD-TYPE"       "8Q LOSS CNV" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-CD-5799        TCGA-CD-5800        TCGA-CD-5801        TCGA-CD-5802 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-CD-5803        TCGA-CG-4300        TCGA-CG-4301        TCGA-CG-4304 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-CG-4305        TCGA-CG-4306        TCGA-CG-4436        TCGA-CG-4437 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-CG-4438        TCGA-CG-4440        TCGA-CG-4441        TCGA-CG-4443 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-CG-4444        TCGA-CG-4449        TCGA-CG-4455        TCGA-CG-4460 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-CG-4462        TCGA-CG-4465        TCGA-CG-4466        TCGA-CG-4469 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-CG-4472        TCGA-CG-4474        TCGA-CG-4477        TCGA-CG-5716 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-CG-5717        TCGA-CG-5718        TCGA-CG-5719        TCGA-CG-5720 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-CG-5721        TCGA-CG-5722        TCGA-CG-5723        TCGA-CG-5724 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-CG-5725        TCGA-CG-5726        TCGA-CG-5727        TCGA-CG-5728 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-CG-5730        TCGA-CG-5732        TCGA-CG-5733        TCGA-CG-5734 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-D7-5577        TCGA-D7-5578        TCGA-D7-5579        TCGA-D7-6518 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-D7-6519        TCGA-D7-6520        TCGA-D7-6521        TCGA-D7-6522 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-D7-6524        TCGA-D7-6525        TCGA-D7-6526        TCGA-D7-6527 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-D7-6528        TCGA-D7-6815        TCGA-D7-6817        TCGA-D7-6818 
      "8Q LOSS CNV" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-D7-6820        TCGA-D7-6822        TCGA-EQ-5647        TCGA-EQ-8122 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-F1-6177        TCGA-F1-6874        TCGA-F1-6875        TCGA-FP-7735 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-FP-7829        TCGA-FP-7916        TCGA-FP-7998        TCGA-FP-8099 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE"       "8Q LOSS CNV" 
       TCGA-FP-8209        TCGA-FP-8210        TCGA-FP-8631        TCGA-HJ-7597 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-IN-7806        TCGA-IN-7808        TCGA-IP-7968 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-B7-5816        TCGA-B7-5818        TCGA-BR-6452        TCGA-BR-6455 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-BR-6457        TCGA-BR-6458        TCGA-BR-6563        TCGA-BR-6564 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-BR-6565        TCGA-BR-6566        TCGA-BR-6705        TCGA-BR-6706 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-BR-6707        TCGA-BR-6709        TCGA-BR-6710        TCGA-BR-6801 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-BR-6802        TCGA-BR-6803        TCGA-BR-6852        TCGA-BR-7196 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-BR-7197        TCGA-BR-7703        TCGA-BR-7704        TCGA-BR-7707 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-BR-7715        TCGA-BR-7716        TCGA-BR-7717        TCGA-BR-7722 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-BR-7723        TCGA-BR-7851        TCGA-BR-7901        TCGA-BR-7957 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-BR-7958        TCGA-BR-7959        TCGA-BR-8059        TCGA-BR-8060 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-BR-8077        TCGA-BR-8078        TCGA-BR-8080        TCGA-BR-8081 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-BR-8284        TCGA-BR-8285        TCGA-BR-8286        TCGA-BR-8289 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE"       "8Q LOSS CNV" "8Q LOSS WILD-TYPE" 
       TCGA-BR-8291        TCGA-BR-8295        TCGA-BR-8296        TCGA-BR-8297 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-BR-8592        TCGA-BR-A4IU        TCGA-BR-A4IV        TCGA-BR-A4IY 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-BR-A4IZ        TCGA-BR-A4J1        TCGA-BR-A4J2        TCGA-BR-A4J4 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-BR-A4J5        TCGA-BR-A4J6        TCGA-BR-A4J8        TCGA-BR-A4J9 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-BR-A4PF        TCGA-BR-A4QI        TCGA-BR-A4QL        TCGA-CD-5798 
"8Q LOSS WILD-TYPE"       "8Q LOSS CNV" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-CD-5799        TCGA-CD-5800        TCGA-CD-5801        TCGA-CD-5802 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-CD-5803        TCGA-CG-4300        TCGA-CG-4301        TCGA-CG-4304 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-CG-4305        TCGA-CG-4306        TCGA-CG-4436        TCGA-CG-4437 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-CG-4438        TCGA-CG-4440        TCGA-CG-4441        TCGA-CG-4443 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-CG-4444        TCGA-CG-4449        TCGA-CG-4455        TCGA-CG-4460 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-CG-4462        TCGA-CG-4465        TCGA-CG-4466        TCGA-CG-4469 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-CG-4472        TCGA-CG-4474        TCGA-CG-4477        TCGA-CG-5716 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-CG-5717        TCGA-CG-5718        TCGA-CG-5719        TCGA-CG-5720 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-CG-5721        TCGA-CG-5722        TCGA-CG-5723        TCGA-CG-5724 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-CG-5725        TCGA-CG-5726        TCGA-CG-5727        TCGA-CG-5728 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-CG-5730        TCGA-CG-5732        TCGA-CG-5733        TCGA-CG-5734 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-D7-5577        TCGA-D7-5578        TCGA-D7-5579        TCGA-D7-6518 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-D7-6519        TCGA-D7-6520        TCGA-D7-6521        TCGA-D7-6522 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-D7-6524        TCGA-D7-6525        TCGA-D7-6526        TCGA-D7-6527 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-D7-6528        TCGA-D7-6815        TCGA-D7-6817        TCGA-D7-6818 
      "8Q LOSS CNV" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-D7-6820        TCGA-D7-6822        TCGA-EQ-5647        TCGA-EQ-8122 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-F1-6177        TCGA-F1-6874        TCGA-F1-6875        TCGA-FP-7735 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-FP-7829        TCGA-FP-7916        TCGA-FP-7998        TCGA-FP-8099 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE"       "8Q LOSS CNV" 
       TCGA-FP-8209        TCGA-FP-8210        TCGA-FP-8631        TCGA-HJ-7597 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-IN-7806        TCGA-IN-7808        TCGA-IP-7968 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-B7-5816        TCGA-B7-5818        TCGA-BR-6452        TCGA-BR-6455 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-BR-6457        TCGA-BR-6458        TCGA-BR-6563        TCGA-BR-6564 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-BR-6565        TCGA-BR-6566        TCGA-BR-6705        TCGA-BR-6706 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-BR-6707        TCGA-BR-6709        TCGA-BR-6710        TCGA-BR-6801 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-BR-6802        TCGA-BR-6803        TCGA-BR-6852        TCGA-BR-7196 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-BR-7197        TCGA-BR-7703        TCGA-BR-7704        TCGA-BR-7707 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-BR-7715        TCGA-BR-7716        TCGA-BR-7717        TCGA-BR-7722 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-BR-7723        TCGA-BR-7851        TCGA-BR-7901        TCGA-BR-7957 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-BR-7958        TCGA-BR-7959        TCGA-BR-8059        TCGA-BR-8060 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-BR-8077        TCGA-BR-8078        TCGA-BR-8080        TCGA-BR-8081 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-BR-8284        TCGA-BR-8285        TCGA-BR-8286        TCGA-BR-8289 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE"       "8Q LOSS CNV" "8Q LOSS WILD-TYPE" 
       TCGA-BR-8291        TCGA-BR-8295        TCGA-BR-8296        TCGA-BR-8297 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-BR-8592        TCGA-BR-A4IU        TCGA-BR-A4IV        TCGA-BR-A4IY 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-BR-A4IZ        TCGA-BR-A4J1        TCGA-BR-A4J2        TCGA-BR-A4J4 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-BR-A4J5        TCGA-BR-A4J6        TCGA-BR-A4J8        TCGA-BR-A4J9 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-BR-A4PF        TCGA-BR-A4QI        TCGA-BR-A4QL        TCGA-CD-5798 
"8Q LOSS WILD-TYPE"       "8Q LOSS CNV" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-CD-5799        TCGA-CD-5800        TCGA-CD-5801        TCGA-CD-5802 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-CD-5803        TCGA-CG-4300        TCGA-CG-4301        TCGA-CG-4304 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-CG-4305        TCGA-CG-4306        TCGA-CG-4436        TCGA-CG-4437 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-CG-4438        TCGA-CG-4440        TCGA-CG-4441        TCGA-CG-4443 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-CG-4444        TCGA-CG-4449        TCGA-CG-4455        TCGA-CG-4460 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-CG-4462        TCGA-CG-4465        TCGA-CG-4466        TCGA-CG-4469 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-CG-4472        TCGA-CG-4474        TCGA-CG-4477        TCGA-CG-5716 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-CG-5717        TCGA-CG-5718        TCGA-CG-5719        TCGA-CG-5720 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-CG-5721        TCGA-CG-5722        TCGA-CG-5723        TCGA-CG-5724 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-CG-5725        TCGA-CG-5726        TCGA-CG-5727        TCGA-CG-5728 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-CG-5730        TCGA-CG-5732        TCGA-CG-5733        TCGA-CG-5734 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-D7-5577        TCGA-D7-5578        TCGA-D7-5579        TCGA-D7-6518 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-D7-6519        TCGA-D7-6520        TCGA-D7-6521        TCGA-D7-6522 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-D7-6524        TCGA-D7-6525        TCGA-D7-6526        TCGA-D7-6527 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-D7-6528        TCGA-D7-6815        TCGA-D7-6817        TCGA-D7-6818 
      "8Q LOSS CNV" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-D7-6820        TCGA-D7-6822        TCGA-EQ-5647        TCGA-EQ-8122 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-F1-6177        TCGA-F1-6874        TCGA-F1-6875        TCGA-FP-7735 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-FP-7829        TCGA-FP-7916        TCGA-FP-7998        TCGA-FP-8099 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE"       "8Q LOSS CNV" 
       TCGA-FP-8209        TCGA-FP-8210        TCGA-FP-8631        TCGA-HJ-7597 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-IN-7806        TCGA-IN-7808        TCGA-IP-7968 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
[1] "hr="     "3400000"
D51V2, continuous
D51V3, binary
[1] "tbl2"
                   cls
clus                [,1] [,2]
  8Q LOSS CNV          2    4
  8Q LOSS WILD-TYPE   70  104
        clus
vv       8Q LOSS CNV 8Q LOSS WILD-TYPE
  FEMALE           2                70
  MALE             4               104
                   vv
clus                STOMACH  ADENOCARCINOMA  DIFFUSE TYPE
  8Q LOSS CNV                                           0
  8Q LOSS WILD-TYPE                                    10
                   vv
clus                STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  8Q LOSS CNV                                                            3
  8Q LOSS WILD-TYPE                                                     13
                   vv
clus                STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  8Q LOSS CNV                                                                       0
  8Q LOSS WILD-TYPE                                                                 8
                   vv
clus                STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE
  8Q LOSS CNV                                                              0
  8Q LOSS WILD-TYPE                                                        3
                   vv
clus                STOMACH ADENOCARCINOMA  SIGNET RING TYPE
  8Q LOSS CNV                                              0
  8Q LOSS WILD-TYPE                                        1
                   vv
clus                STOMACH ADENOCARCINOMA - DIFFUSE TYPE
  8Q LOSS CNV                                           0
  8Q LOSS WILD-TYPE                                    16
                   vv
clus                STOMACH ADENOCARCINOMA - NOT OTHERWISE SPECIFIED (NOS)
  8Q LOSS CNV                                                            1
  8Q LOSS WILD-TYPE                                                     72
                   vv
clus                STOMACH INTESTINAL ADENOCARCINOMA - MUCINOUS TYPE
  8Q LOSS CNV                                                       0
  8Q LOSS WILD-TYPE                                                 7
                   vv
clus                STOMACH INTESTINAL ADENOCARCINOMA - PAPILLARY TYPE
  8Q LOSS CNV                                                        0
  8Q LOSS WILD-TYPE                                                  3
                   vv
clus                STOMACH INTESTINAL ADENOCARCINOMA - TUBULAR TYPE
  8Q LOSS CNV                                                      2
  8Q LOSS WILD-TYPE                                                8
                   vv
clus                STOMACH INTESTINAL ADENOCARCINOMA - TYPE NOT OTHERWISE SPECIFIED (NOS)
  8Q LOSS CNV                                                                            0
  8Q LOSS WILD-TYPE                                                                     28
D51V4, multiclass
                   vv
clus                T1 T2 T3 T4
  8Q LOSS CNV        0  2  0  0
  8Q LOSS WILD-TYPE  6 50 56 18
D51V5, multiclass
[1] "Remove cluster labels:" "8Q LOSS CNV"           
clus
      8Q LOSS CNV 8Q LOSS WILD-TYPE 
                2               130 
       TCGA-B7-5816        TCGA-B7-5818        TCGA-BR-4183        TCGA-BR-4184 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-BR-4201        TCGA-BR-4253        TCGA-BR-4255        TCGA-BR-4267 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-BR-4279        TCGA-BR-4280        TCGA-BR-4292        TCGA-BR-4357 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-BR-4361        TCGA-BR-4363        TCGA-BR-4368        TCGA-BR-4371 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-BR-6452        TCGA-BR-6453        TCGA-BR-6454        TCGA-BR-6455 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-BR-6456        TCGA-BR-6457        TCGA-BR-6458        TCGA-BR-6563 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-BR-6564        TCGA-BR-6565        TCGA-BR-6566        TCGA-BR-6705 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-BR-6706        TCGA-BR-6707        TCGA-BR-6709        TCGA-BR-6710 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-BR-6801        TCGA-BR-6802        TCGA-BR-6803        TCGA-BR-6852 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-BR-7196        TCGA-BR-7197        TCGA-BR-7703        TCGA-BR-7704 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-BR-7707        TCGA-BR-7715        TCGA-BR-7716        TCGA-BR-7717 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-BR-7722        TCGA-BR-7723        TCGA-BR-7851        TCGA-BR-7901 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-BR-7957        TCGA-CD-5798        TCGA-CD-5799        TCGA-CD-5800 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-CD-5801        TCGA-CD-5802        TCGA-CD-5803        TCGA-CD-5804 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-CG-4300        TCGA-CG-4301        TCGA-CG-4304        TCGA-CG-4305 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-CG-4306        TCGA-CG-4436        TCGA-CG-4437        TCGA-CG-4438 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-CG-4440        TCGA-CG-4441        TCGA-CG-4442        TCGA-CG-4443 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-CG-4444        TCGA-CG-4449        TCGA-CG-4455        TCGA-CG-4460 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-CG-4462        TCGA-CG-4465        TCGA-CG-4466        TCGA-CG-4469 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-CG-4472        TCGA-CG-4474        TCGA-CG-4475        TCGA-CG-4476 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-CG-4477        TCGA-CG-5716        TCGA-CG-5717        TCGA-CG-5718 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-CG-5719        TCGA-CG-5720        TCGA-CG-5721        TCGA-CG-5722 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-CG-5723        TCGA-CG-5724        TCGA-CG-5725        TCGA-CG-5726 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-CG-5727        TCGA-CG-5728        TCGA-CG-5730        TCGA-CG-5732 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-CG-5733        TCGA-CG-5734        TCGA-D7-5577        TCGA-D7-5578 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-D7-5579        TCGA-D7-6518        TCGA-D7-6519        TCGA-D7-6520 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-D7-6521        TCGA-D7-6522        TCGA-D7-6524        TCGA-D7-6525 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-D7-6526        TCGA-D7-6527        TCGA-D7-6815        TCGA-D7-6817 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-D7-6818        TCGA-D7-6820        TCGA-D7-6822        TCGA-EQ-5647 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-F1-6177        TCGA-F1-6874        TCGA-F1-6875        TCGA-FP-7735 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-FP-7829        TCGA-FP-7998        TCGA-HF-7131        TCGA-HF-7132 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-HF-7133        TCGA-HF-7134        TCGA-HF-7136        TCGA-IN-7806 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-IN-7808        TCGA-IP-7968 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
                   vv
clus                N0 N1 N2 N3
  8Q LOSS CNV        1  1  0  0
  8Q LOSS WILD-TYPE 43 48 23 15
D51V6, multiclass
[1] "Remove cluster labels:" "8Q LOSS CNV"           
clus
      8Q LOSS CNV 8Q LOSS WILD-TYPE 
                2               129 
       TCGA-B7-5816        TCGA-B7-5818        TCGA-BR-4183        TCGA-BR-4184 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-BR-4188        TCGA-BR-4253        TCGA-BR-4255        TCGA-BR-4256 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-BR-4267        TCGA-BR-4279        TCGA-BR-4280        TCGA-BR-4361 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-BR-4362        TCGA-BR-4367        TCGA-BR-4368        TCGA-BR-6452 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-BR-6453        TCGA-BR-6454        TCGA-BR-6455        TCGA-BR-6456 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-BR-6457        TCGA-BR-6458        TCGA-BR-6563        TCGA-BR-6564 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-BR-6565        TCGA-BR-6566        TCGA-BR-6705        TCGA-BR-6706 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-BR-6707        TCGA-BR-6709        TCGA-BR-6710        TCGA-BR-6801 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-BR-6802        TCGA-BR-6803        TCGA-BR-6852        TCGA-BR-7196 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-BR-7197        TCGA-BR-7703        TCGA-BR-7704        TCGA-BR-7707 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-BR-7715        TCGA-BR-7716        TCGA-BR-7717        TCGA-BR-7722 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-BR-7723        TCGA-BR-7851        TCGA-BR-7901        TCGA-BR-7957 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-CD-5798        TCGA-CD-5799        TCGA-CD-5800        TCGA-CD-5801 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-CD-5802        TCGA-CD-5803        TCGA-CD-5804        TCGA-CG-4300 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-CG-4301        TCGA-CG-4304        TCGA-CG-4305        TCGA-CG-4306 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-CG-4436        TCGA-CG-4437        TCGA-CG-4438        TCGA-CG-4440 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-CG-4441        TCGA-CG-4442        TCGA-CG-4443        TCGA-CG-4444 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-CG-4449        TCGA-CG-4455        TCGA-CG-4460        TCGA-CG-4462 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-CG-4465        TCGA-CG-4466        TCGA-CG-4469        TCGA-CG-4472 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-CG-4474        TCGA-CG-4475        TCGA-CG-4476        TCGA-CG-4477 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-CG-5716        TCGA-CG-5717        TCGA-CG-5718        TCGA-CG-5719 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-CG-5720        TCGA-CG-5721        TCGA-CG-5722        TCGA-CG-5723 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-CG-5724        TCGA-CG-5725        TCGA-CG-5726        TCGA-CG-5727 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-CG-5728        TCGA-CG-5730        TCGA-CG-5732        TCGA-CG-5733 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-CG-5734        TCGA-D7-5577        TCGA-D7-5578        TCGA-D7-5579 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-D7-6518        TCGA-D7-6519        TCGA-D7-6520        TCGA-D7-6521 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-D7-6522        TCGA-D7-6524        TCGA-D7-6525        TCGA-D7-6526 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-D7-6527        TCGA-D7-6815        TCGA-D7-6817        TCGA-D7-6818 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-D7-6820        TCGA-D7-6822        TCGA-EQ-5647        TCGA-F1-6177 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-F1-6874        TCGA-F1-6875        TCGA-FP-7735        TCGA-FP-7829 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-FP-7998        TCGA-HF-7131        TCGA-HF-7132        TCGA-HF-7133 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-HF-7134        TCGA-HF-7136        TCGA-IN-7806        TCGA-IN-7808 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-IP-7968 
"8Q LOSS WILD-TYPE" 
                   vv
clus                 M0  M1  MX
  8Q LOSS CNV         3   0   0
  8Q LOSS WILD-TYPE 115  16   8
D51V7, multiclass
    clus
vv   8Q LOSS CNV 8Q LOSS WILD-TYPE
  M0           3               115
  M1           0                16
  MX           0                 8
                   vv
clus                 I II III IV
  8Q LOSS CNV        1  0   0  0
  8Q LOSS WILD-TYPE 23 37  39 26
D51V8, multiclass
[1] "Remove cluster labels:" "8Q LOSS CNV"           
clus
      8Q LOSS CNV 8Q LOSS WILD-TYPE 
                1               125 
       TCGA-B7-5816        TCGA-B7-5818        TCGA-BR-4183        TCGA-BR-4184 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-BR-4253        TCGA-BR-4255        TCGA-BR-4267        TCGA-BR-4279 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-BR-4280        TCGA-BR-4361        TCGA-BR-4368        TCGA-BR-6452 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-BR-6453        TCGA-BR-6454        TCGA-BR-6455        TCGA-BR-6456 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-BR-6457        TCGA-BR-6458        TCGA-BR-6563        TCGA-BR-6564 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-BR-6565        TCGA-BR-6566        TCGA-BR-6705        TCGA-BR-6706 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-BR-6707        TCGA-BR-6709        TCGA-BR-6710        TCGA-BR-6801 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-BR-6802        TCGA-BR-6803        TCGA-BR-6852        TCGA-BR-7196 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-BR-7197        TCGA-BR-7703        TCGA-BR-7704        TCGA-BR-7707 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-BR-7715        TCGA-BR-7716        TCGA-BR-7717        TCGA-BR-7722 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-BR-7723        TCGA-BR-7851        TCGA-BR-7901        TCGA-BR-7957 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-CD-5798        TCGA-CD-5799        TCGA-CD-5800        TCGA-CD-5801 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-CD-5802        TCGA-CD-5803        TCGA-CD-5804        TCGA-CG-4300 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-CG-4301        TCGA-CG-4304        TCGA-CG-4305        TCGA-CG-4306 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-CG-4436        TCGA-CG-4437        TCGA-CG-4438        TCGA-CG-4440 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-CG-4441        TCGA-CG-4442        TCGA-CG-4443        TCGA-CG-4444 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-CG-4449        TCGA-CG-4455        TCGA-CG-4460        TCGA-CG-4462 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-CG-4465        TCGA-CG-4466        TCGA-CG-4469        TCGA-CG-4472 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-CG-4474        TCGA-CG-4475        TCGA-CG-4476        TCGA-CG-4477 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-CG-5716        TCGA-CG-5717        TCGA-CG-5718        TCGA-CG-5719 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-CG-5720        TCGA-CG-5721        TCGA-CG-5722        TCGA-CG-5723 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-CG-5724        TCGA-CG-5725        TCGA-CG-5726        TCGA-CG-5727 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-CG-5728        TCGA-CG-5730        TCGA-CG-5732        TCGA-CG-5733 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-CG-5734        TCGA-D7-5577        TCGA-D7-5578        TCGA-D7-5579 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-D7-6518        TCGA-D7-6519        TCGA-D7-6520        TCGA-D7-6521 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-D7-6522        TCGA-D7-6524        TCGA-D7-6525        TCGA-D7-6526 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-D7-6527        TCGA-D7-6815        TCGA-D7-6817        TCGA-D7-6818 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-D7-6820        TCGA-D7-6822        TCGA-EQ-5647        TCGA-F1-6177 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-F1-6874        TCGA-F1-6875        TCGA-FP-7735        TCGA-FP-7829 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-FP-7998        TCGA-HF-7131        TCGA-HF-7132        TCGA-HF-7133 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-HF-7134        TCGA-HF-7136        TCGA-IN-7806        TCGA-IN-7808 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-IP-7968 
"8Q LOSS WILD-TYPE" 
D51V9, binary
[1] "tbl2"
                   cls
clus                [,1] [,2]
  8Q LOSS CNV          0    6
  8Q LOSS WILD-TYPE    5  169
     clus
vv    8Q LOSS CNV 8Q LOSS WILD-TYPE
  NO            0                 5
  YES           6               169
                   vv
clus                 R0  R1  R2  RX
  8Q LOSS CNV         4   0   0   2
  8Q LOSS WILD-TYPE 121   7  12  23
D51V10, multiclass
    clus
vv   8Q LOSS CNV 8Q LOSS WILD-TYPE
  R0           4               121
  R1           0                 7
  R2           0                12
  RX           2                23
D51V11, continuous

Clustering(52) Variable = 9p loss
D52V1, survival
                   sevent
clus2                0  1
  9P LOSS CNV       25  3
  9P LOSS WILD-TYPE 99 16
      9P LOSS CNV 9P LOSS WILD-TYPE 
               28               115 
      9P LOSS CNV 9P LOSS WILD-TYPE 
                3                16 
$`9P LOSS CNV`
TCGA-BR-7197 TCGA-BR-8060 TCGA-BR-8077 TCGA-BR-8291 TCGA-BR-A4J1 TCGA-BR-A4J6 
        1.48         1.32         0.69         1.18         0.72         0.13 
TCGA-CD-5799 TCGA-CG-4438 TCGA-CG-4443 TCGA-CG-4449 TCGA-CG-4466 TCGA-CG-4472 
        0.69        54.05        29.98        19.07        18.94        12.00 
TCGA-CG-5718 TCGA-CG-5719 TCGA-CG-5725 TCGA-CG-5730 TCGA-CG-5732 TCGA-D7-6519 
        1.02         1.02        15.02         4.01        55.04        15.65 
TCGA-D7-6520 TCGA-D7-6521 TCGA-D7-6525 TCGA-D7-6526 TCGA-D7-6817 TCGA-EQ-8122 
        9.63         8.19         5.95         6.61         4.70         7.79 
TCGA-F1-6875 TCGA-FP-8099 TCGA-FP-8631 TCGA-IN-7806 
       72.23         1.02         0.56         6.87 

$`9P LOSS WILD-TYPE`
TCGA-B7-5816 TCGA-B7-5818 TCGA-BR-6452 TCGA-BR-6455 TCGA-BR-6457 TCGA-BR-6458 
        5.62         0.10         0.95         1.41         1.35         1.35 
TCGA-BR-6563 TCGA-BR-6564 TCGA-BR-6565 TCGA-BR-6566 TCGA-BR-6705 TCGA-BR-6706 
        0.85         0.82         0.62         0.62         1.71         2.17 
TCGA-BR-6707 TCGA-BR-6709 TCGA-BR-6710 TCGA-BR-6801 TCGA-BR-6802 TCGA-BR-6803 
        0.99         1.22         0.66         1.12         0.76         0.66 
TCGA-BR-6852 TCGA-BR-7196 TCGA-BR-7703 TCGA-BR-7704 TCGA-BR-7707 TCGA-BR-7715 
        0.26         1.22         0.46         1.25         0.13         1.05 
TCGA-BR-7716 TCGA-BR-7717 TCGA-BR-7722 TCGA-BR-7723 TCGA-BR-7851 TCGA-BR-7901 
        0.82         0.69         0.16         4.54         0.99         0.95 
TCGA-BR-7957 TCGA-BR-7958 TCGA-BR-7959 TCGA-BR-8059 TCGA-BR-8078 TCGA-BR-8080 
        0.69         0.16         1.08         0.82         0.95         0.49 
TCGA-BR-8081 TCGA-BR-8284 TCGA-BR-8285 TCGA-BR-8286 TCGA-BR-8289 TCGA-BR-8295 
        0.46         0.72         0.26         0.43         0.26         1.55 
TCGA-BR-8296 TCGA-BR-8297 TCGA-BR-8592 TCGA-BR-A4IU TCGA-BR-A4IV TCGA-BR-A4IY 
        1.48         0.76         0.20         0.59         0.92         0.39 
TCGA-BR-A4IZ TCGA-BR-A4J2 TCGA-BR-A4J4 TCGA-BR-A4J5 TCGA-BR-A4J8 TCGA-BR-A4J9 
        0.79         0.79         0.53         0.43         0.23         0.10 
TCGA-BR-A4PF TCGA-BR-A4QI TCGA-BR-A4QL TCGA-CD-5798 TCGA-CD-5800 TCGA-CD-5801 
        0.72         0.49         2.24         0.82         0.36         0.49 
TCGA-CD-5802 TCGA-CD-5803 TCGA-CG-4300 TCGA-CG-4301 TCGA-CG-4304 TCGA-CG-4305 
        0.30         0.07        20.02         3.02        27.02        15.95 
TCGA-CG-4306 TCGA-CG-4436 TCGA-CG-4437 TCGA-CG-4440 TCGA-CG-4441 TCGA-CG-4444 
        1.02        52.96         8.05         4.01        14.01        47.05 
TCGA-CG-4455 TCGA-CG-4460 TCGA-CG-4462 TCGA-CG-4465 TCGA-CG-4469 TCGA-CG-4474 
       12.03        21.99         1.02         8.98         7.07         1.02 
TCGA-CG-4477 TCGA-CG-5716 TCGA-CG-5717 TCGA-CG-5720 TCGA-CG-5721 TCGA-CG-5722 
        1.02         1.02         6.94         0.99         5.98         0.95 
TCGA-CG-5723 TCGA-CG-5724 TCGA-CG-5726 TCGA-CG-5727 TCGA-CG-5728 TCGA-CG-5733 
       70.06        12.03        28.96        31.04        65.10        21.07 
TCGA-CG-5734 TCGA-D7-5577 TCGA-D7-5578 TCGA-D7-5579 TCGA-D7-6518 TCGA-D7-6522 
        7.99         8.65         3.58         4.54         9.80         6.90 
TCGA-D7-6524 TCGA-D7-6527 TCGA-D7-6528 TCGA-D7-6815 TCGA-D7-6818 TCGA-D7-6820 
        0.69         4.14         1.68         3.65         4.04         2.93 
TCGA-D7-6822 TCGA-EQ-5647 TCGA-F1-6177 TCGA-F1-6874 TCGA-FP-7735 TCGA-FP-7829 
        4.27         0.62         6.54         2.01         0.39         0.20 
TCGA-FP-7916 TCGA-FP-7998 TCGA-FP-8209 TCGA-FP-8210 TCGA-HJ-7597 TCGA-IN-7808 
        3.02         3.58        59.05         5.03        26.43         3.55 
TCGA-IP-7968 
        2.53 

      9P LOSS CNV 9P LOSS WILD-TYPE 
             0.13              0.07 
      9P LOSS CNV 9P LOSS WILD-TYPE 
            72.23             70.06 
      9P LOSS CNV 9P LOSS WILD-TYPE 
             6.28              1.05 
[1] "0.1 - 72.2 (6.3)" "0.1 - 70.1 (1.1)"
       TCGA-B7-5816        TCGA-B7-5818        TCGA-BR-6452        TCGA-BR-6455 
"9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" 
       TCGA-BR-6457        TCGA-BR-6458        TCGA-BR-6563        TCGA-BR-6564 
"9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" 
       TCGA-BR-6565        TCGA-BR-6566        TCGA-BR-6705        TCGA-BR-6706 
"9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" 
       TCGA-BR-6707        TCGA-BR-6709        TCGA-BR-6710        TCGA-BR-6801 
"9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" 
       TCGA-BR-6802        TCGA-BR-6803        TCGA-BR-6852        TCGA-BR-7196 
"9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" 
       TCGA-BR-7197        TCGA-BR-7703        TCGA-BR-7704        TCGA-BR-7707 
      "9P LOSS CNV" "9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" 
       TCGA-BR-7715        TCGA-BR-7716        TCGA-BR-7717        TCGA-BR-7722 
"9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" 
       TCGA-BR-7723        TCGA-BR-7851        TCGA-BR-7901        TCGA-BR-7957 
"9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" 
       TCGA-BR-7958        TCGA-BR-7959        TCGA-BR-8059        TCGA-BR-8060 
"9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE"       "9P LOSS CNV" 
       TCGA-BR-8077        TCGA-BR-8078        TCGA-BR-8080        TCGA-BR-8081 
      "9P LOSS CNV" "9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" 
       TCGA-BR-8284        TCGA-BR-8285        TCGA-BR-8286        TCGA-BR-8289 
"9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" 
       TCGA-BR-8291        TCGA-BR-8295        TCGA-BR-8296        TCGA-BR-8297 
      "9P LOSS CNV" "9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" 
       TCGA-BR-8592        TCGA-BR-A4IU        TCGA-BR-A4IV        TCGA-BR-A4IY 
"9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" 
       TCGA-BR-A4IZ        TCGA-BR-A4J1        TCGA-BR-A4J2        TCGA-BR-A4J4 
"9P LOSS WILD-TYPE"       "9P LOSS CNV" "9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" 
       TCGA-BR-A4J5        TCGA-BR-A4J6        TCGA-BR-A4J8        TCGA-BR-A4J9 
"9P LOSS WILD-TYPE"       "9P LOSS CNV" "9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" 
       TCGA-BR-A4PF        TCGA-BR-A4QI        TCGA-BR-A4QL        TCGA-CD-5798 
"9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" 
       TCGA-CD-5799        TCGA-CD-5800        TCGA-CD-5801        TCGA-CD-5802 
      "9P LOSS CNV" "9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" 
       TCGA-CD-5803        TCGA-CG-4300        TCGA-CG-4301        TCGA-CG-4304 
"9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" 
       TCGA-CG-4305        TCGA-CG-4306        TCGA-CG-4436        TCGA-CG-4437 
"9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" 
       TCGA-CG-4438        TCGA-CG-4440        TCGA-CG-4441        TCGA-CG-4443 
      "9P LOSS CNV" "9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE"       "9P LOSS CNV" 
       TCGA-CG-4444        TCGA-CG-4449        TCGA-CG-4455        TCGA-CG-4460 
"9P LOSS WILD-TYPE"       "9P LOSS CNV" "9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" 
       TCGA-CG-4462        TCGA-CG-4465        TCGA-CG-4466        TCGA-CG-4469 
"9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE"       "9P LOSS CNV" "9P LOSS WILD-TYPE" 
       TCGA-CG-4472        TCGA-CG-4474        TCGA-CG-4477        TCGA-CG-5716 
      "9P LOSS CNV" "9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" 
       TCGA-CG-5717        TCGA-CG-5718        TCGA-CG-5719        TCGA-CG-5720 
"9P LOSS WILD-TYPE"       "9P LOSS CNV"       "9P LOSS CNV" "9P LOSS WILD-TYPE" 
       TCGA-CG-5721        TCGA-CG-5722        TCGA-CG-5723        TCGA-CG-5724 
"9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" 
       TCGA-CG-5725        TCGA-CG-5726        TCGA-CG-5727        TCGA-CG-5728 
      "9P LOSS CNV" "9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" 
       TCGA-CG-5730        TCGA-CG-5732        TCGA-CG-5733        TCGA-CG-5734 
      "9P LOSS CNV"       "9P LOSS CNV" "9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" 
       TCGA-D7-5577        TCGA-D7-5578        TCGA-D7-5579        TCGA-D7-6518 
"9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" 
       TCGA-D7-6519        TCGA-D7-6520        TCGA-D7-6521        TCGA-D7-6522 
      "9P LOSS CNV"       "9P LOSS CNV"       "9P LOSS CNV" "9P LOSS WILD-TYPE" 
       TCGA-D7-6524        TCGA-D7-6525        TCGA-D7-6526        TCGA-D7-6527 
"9P LOSS WILD-TYPE"       "9P LOSS CNV"       "9P LOSS CNV" "9P LOSS WILD-TYPE" 
       TCGA-D7-6528        TCGA-D7-6815        TCGA-D7-6817        TCGA-D7-6818 
"9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE"       "9P LOSS CNV" "9P LOSS WILD-TYPE" 
       TCGA-D7-6820        TCGA-D7-6822        TCGA-EQ-5647        TCGA-EQ-8122 
"9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE"       "9P LOSS CNV" 
       TCGA-F1-6177        TCGA-F1-6874        TCGA-F1-6875        TCGA-FP-7735 
"9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE"       "9P LOSS CNV" "9P LOSS WILD-TYPE" 
       TCGA-FP-7829        TCGA-FP-7916        TCGA-FP-7998        TCGA-FP-8099 
"9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE"       "9P LOSS CNV" 
       TCGA-FP-8209        TCGA-FP-8210        TCGA-FP-8631        TCGA-HJ-7597 
"9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE"       "9P LOSS CNV" "9P LOSS WILD-TYPE" 
       TCGA-IN-7806        TCGA-IN-7808        TCGA-IP-7968 
      "9P LOSS CNV" "9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" 
       TCGA-B7-5816        TCGA-B7-5818        TCGA-BR-6452        TCGA-BR-6455 
"9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" 
       TCGA-BR-6457        TCGA-BR-6458        TCGA-BR-6563        TCGA-BR-6564 
"9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" 
       TCGA-BR-6565        TCGA-BR-6566        TCGA-BR-6705        TCGA-BR-6706 
"9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" 
       TCGA-BR-6707        TCGA-BR-6709        TCGA-BR-6710        TCGA-BR-6801 
"9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" 
       TCGA-BR-6802        TCGA-BR-6803        TCGA-BR-6852        TCGA-BR-7196 
"9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" 
       TCGA-BR-7197        TCGA-BR-7703        TCGA-BR-7704        TCGA-BR-7707 
      "9P LOSS CNV" "9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" 
       TCGA-BR-7715        TCGA-BR-7716        TCGA-BR-7717        TCGA-BR-7722 
"9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" 
       TCGA-BR-7723        TCGA-BR-7851        TCGA-BR-7901        TCGA-BR-7957 
"9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" 
       TCGA-BR-7958        TCGA-BR-7959        TCGA-BR-8059        TCGA-BR-8060 
"9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE"       "9P LOSS CNV" 
       TCGA-BR-8077        TCGA-BR-8078        TCGA-BR-8080        TCGA-BR-8081 
      "9P LOSS CNV" "9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" 
       TCGA-BR-8284        TCGA-BR-8285        TCGA-BR-8286        TCGA-BR-8289 
"9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" 
       TCGA-BR-8291        TCGA-BR-8295        TCGA-BR-8296        TCGA-BR-8297 
      "9P LOSS CNV" "9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" 
       TCGA-BR-8592        TCGA-BR-A4IU        TCGA-BR-A4IV        TCGA-BR-A4IY 
"9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" 
       TCGA-BR-A4IZ        TCGA-BR-A4J1        TCGA-BR-A4J2        TCGA-BR-A4J4 
"9P LOSS WILD-TYPE"       "9P LOSS CNV" "9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" 
       TCGA-BR-A4J5        TCGA-BR-A4J6        TCGA-BR-A4J8        TCGA-BR-A4J9 
"9P LOSS WILD-TYPE"       "9P LOSS CNV" "9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" 
       TCGA-BR-A4PF        TCGA-BR-A4QI        TCGA-BR-A4QL        TCGA-CD-5798 
"9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" 
       TCGA-CD-5799        TCGA-CD-5800        TCGA-CD-5801        TCGA-CD-5802 
      "9P LOSS CNV" "9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" 
       TCGA-CD-5803        TCGA-CG-4300        TCGA-CG-4301        TCGA-CG-4304 
"9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" 
       TCGA-CG-4305        TCGA-CG-4306        TCGA-CG-4436        TCGA-CG-4437 
"9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" 
       TCGA-CG-4438        TCGA-CG-4440        TCGA-CG-4441        TCGA-CG-4443 
      "9P LOSS CNV" "9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE"       "9P LOSS CNV" 
       TCGA-CG-4444        TCGA-CG-4449        TCGA-CG-4455        TCGA-CG-4460 
"9P LOSS WILD-TYPE"       "9P LOSS CNV" "9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" 
       TCGA-CG-4462        TCGA-CG-4465        TCGA-CG-4466        TCGA-CG-4469 
"9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE"       "9P LOSS CNV" "9P LOSS WILD-TYPE" 
       TCGA-CG-4472        TCGA-CG-4474        TCGA-CG-4477        TCGA-CG-5716 
      "9P LOSS CNV" "9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" 
       TCGA-CG-5717        TCGA-CG-5718        TCGA-CG-5719        TCGA-CG-5720 
"9P LOSS WILD-TYPE"       "9P LOSS CNV"       "9P LOSS CNV" "9P LOSS WILD-TYPE" 
       TCGA-CG-5721        TCGA-CG-5722        TCGA-CG-5723        TCGA-CG-5724 
"9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" 
       TCGA-CG-5725        TCGA-CG-5726        TCGA-CG-5727        TCGA-CG-5728 
      "9P LOSS CNV" "9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" 
       TCGA-CG-5730        TCGA-CG-5732        TCGA-CG-5733        TCGA-CG-5734 
      "9P LOSS CNV"       "9P LOSS CNV" "9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" 
       TCGA-D7-5577        TCGA-D7-5578        TCGA-D7-5579        TCGA-D7-6518 
"9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" 
       TCGA-D7-6519        TCGA-D7-6520        TCGA-D7-6521        TCGA-D7-6522 
      "9P LOSS CNV"       "9P LOSS CNV"       "9P LOSS CNV" "9P LOSS WILD-TYPE" 
       TCGA-D7-6524        TCGA-D7-6525        TCGA-D7-6526        TCGA-D7-6527 
"9P LOSS WILD-TYPE"       "9P LOSS CNV"       "9P LOSS CNV" "9P LOSS WILD-TYPE" 
       TCGA-D7-6528        TCGA-D7-6815        TCGA-D7-6817        TCGA-D7-6818 
"9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE"       "9P LOSS CNV" "9P LOSS WILD-TYPE" 
       TCGA-D7-6820        TCGA-D7-6822        TCGA-EQ-5647        TCGA-EQ-8122 
"9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE"       "9P LOSS CNV" 
       TCGA-F1-6177        TCGA-F1-6874        TCGA-F1-6875        TCGA-FP-7735 
"9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE"       "9P LOSS CNV" "9P LOSS WILD-TYPE" 
       TCGA-FP-7829        TCGA-FP-7916        TCGA-FP-7998        TCGA-FP-8099 
"9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE"       "9P LOSS CNV" 
       TCGA-FP-8209        TCGA-FP-8210        TCGA-FP-8631        TCGA-HJ-7597 
"9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE"       "9P LOSS CNV" "9P LOSS WILD-TYPE" 
       TCGA-IN-7806        TCGA-IN-7808        TCGA-IP-7968 
      "9P LOSS CNV" "9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" 
       TCGA-B7-5816        TCGA-B7-5818        TCGA-BR-6452        TCGA-BR-6455 
"9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" 
       TCGA-BR-6457        TCGA-BR-6458        TCGA-BR-6563        TCGA-BR-6564 
"9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" 
       TCGA-BR-6565        TCGA-BR-6566        TCGA-BR-6705        TCGA-BR-6706 
"9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" 
       TCGA-BR-6707        TCGA-BR-6709        TCGA-BR-6710        TCGA-BR-6801 
"9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" 
       TCGA-BR-6802        TCGA-BR-6803        TCGA-BR-6852        TCGA-BR-7196 
"9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" 
       TCGA-BR-7197        TCGA-BR-7703        TCGA-BR-7704        TCGA-BR-7707 
      "9P LOSS CNV" "9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" 
       TCGA-BR-7715        TCGA-BR-7716        TCGA-BR-7717        TCGA-BR-7722 
"9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" 
       TCGA-BR-7723        TCGA-BR-7851        TCGA-BR-7901        TCGA-BR-7957 
"9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" 
       TCGA-BR-7958        TCGA-BR-7959        TCGA-BR-8059        TCGA-BR-8060 
"9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE"       "9P LOSS CNV" 
       TCGA-BR-8077        TCGA-BR-8078        TCGA-BR-8080        TCGA-BR-8081 
      "9P LOSS CNV" "9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" 
       TCGA-BR-8284        TCGA-BR-8285        TCGA-BR-8286        TCGA-BR-8289 
"9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" 
       TCGA-BR-8291        TCGA-BR-8295        TCGA-BR-8296        TCGA-BR-8297 
      "9P LOSS CNV" "9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" 
       TCGA-BR-8592        TCGA-BR-A4IU        TCGA-BR-A4IV        TCGA-BR-A4IY 
"9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" 
       TCGA-BR-A4IZ        TCGA-BR-A4J1        TCGA-BR-A4J2        TCGA-BR-A4J4 
"9P LOSS WILD-TYPE"       "9P LOSS CNV" "9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" 
       TCGA-BR-A4J5        TCGA-BR-A4J6        TCGA-BR-A4J8        TCGA-BR-A4J9 
"9P LOSS WILD-TYPE"       "9P LOSS CNV" "9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" 
       TCGA-BR-A4PF        TCGA-BR-A4QI        TCGA-BR-A4QL        TCGA-CD-5798 
"9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" 
       TCGA-CD-5799        TCGA-CD-5800        TCGA-CD-5801        TCGA-CD-5802 
      "9P LOSS CNV" "9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" 
       TCGA-CD-5803        TCGA-CG-4300        TCGA-CG-4301        TCGA-CG-4304 
"9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" 
       TCGA-CG-4305        TCGA-CG-4306        TCGA-CG-4436        TCGA-CG-4437 
"9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" 
       TCGA-CG-4438        TCGA-CG-4440        TCGA-CG-4441        TCGA-CG-4443 
      "9P LOSS CNV" "9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE"       "9P LOSS CNV" 
       TCGA-CG-4444        TCGA-CG-4449        TCGA-CG-4455        TCGA-CG-4460 
"9P LOSS WILD-TYPE"       "9P LOSS CNV" "9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" 
       TCGA-CG-4462        TCGA-CG-4465        TCGA-CG-4466        TCGA-CG-4469 
"9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE"       "9P LOSS CNV" "9P LOSS WILD-TYPE" 
       TCGA-CG-4472        TCGA-CG-4474        TCGA-CG-4477        TCGA-CG-5716 
      "9P LOSS CNV" "9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" 
       TCGA-CG-5717        TCGA-CG-5718        TCGA-CG-5719        TCGA-CG-5720 
"9P LOSS WILD-TYPE"       "9P LOSS CNV"       "9P LOSS CNV" "9P LOSS WILD-TYPE" 
       TCGA-CG-5721        TCGA-CG-5722        TCGA-CG-5723        TCGA-CG-5724 
"9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" 
       TCGA-CG-5725        TCGA-CG-5726        TCGA-CG-5727        TCGA-CG-5728 
      "9P LOSS CNV" "9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" 
       TCGA-CG-5730        TCGA-CG-5732        TCGA-CG-5733        TCGA-CG-5734 
      "9P LOSS CNV"       "9P LOSS CNV" "9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" 
       TCGA-D7-5577        TCGA-D7-5578        TCGA-D7-5579        TCGA-D7-6518 
"9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" 
       TCGA-D7-6519        TCGA-D7-6520        TCGA-D7-6521        TCGA-D7-6522 
      "9P LOSS CNV"       "9P LOSS CNV"       "9P LOSS CNV" "9P LOSS WILD-TYPE" 
       TCGA-D7-6524        TCGA-D7-6525        TCGA-D7-6526        TCGA-D7-6527 
"9P LOSS WILD-TYPE"       "9P LOSS CNV"       "9P LOSS CNV" "9P LOSS WILD-TYPE" 
       TCGA-D7-6528        TCGA-D7-6815        TCGA-D7-6817        TCGA-D7-6818 
"9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE"       "9P LOSS CNV" "9P LOSS WILD-TYPE" 
       TCGA-D7-6820        TCGA-D7-6822        TCGA-EQ-5647        TCGA-EQ-8122 
"9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE"       "9P LOSS CNV" 
       TCGA-F1-6177        TCGA-F1-6874        TCGA-F1-6875        TCGA-FP-7735 
"9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE"       "9P LOSS CNV" "9P LOSS WILD-TYPE" 
       TCGA-FP-7829        TCGA-FP-7916        TCGA-FP-7998        TCGA-FP-8099 
"9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE"       "9P LOSS CNV" 
       TCGA-FP-8209        TCGA-FP-8210        TCGA-FP-8631        TCGA-HJ-7597 
"9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE"       "9P LOSS CNV" "9P LOSS WILD-TYPE" 
       TCGA-IN-7806        TCGA-IN-7808        TCGA-IP-7968 
      "9P LOSS CNV" "9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" 
[1] "hr=" "3.7"
D52V2, continuous
D52V3, binary
[1] "tbl2"
                   cls
clus                [,1] [,2]
  9P LOSS CNV         11   21
  9P LOSS WILD-TYPE   61   87
        clus
vv       9P LOSS CNV 9P LOSS WILD-TYPE
  FEMALE          11                61
  MALE            21                87
                   vv
clus                STOMACH  ADENOCARCINOMA  DIFFUSE TYPE
  9P LOSS CNV                                           1
  9P LOSS WILD-TYPE                                     9
                   vv
clus                STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  9P LOSS CNV                                                            4
  9P LOSS WILD-TYPE                                                     12
                   vv
clus                STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  9P LOSS CNV                                                                       3
  9P LOSS WILD-TYPE                                                                 5
                   vv
clus                STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE
  9P LOSS CNV                                                              0
  9P LOSS WILD-TYPE                                                        3
                   vv
clus                STOMACH ADENOCARCINOMA  SIGNET RING TYPE
  9P LOSS CNV                                              0
  9P LOSS WILD-TYPE                                        1
                   vv
clus                STOMACH ADENOCARCINOMA - DIFFUSE TYPE
  9P LOSS CNV                                           4
  9P LOSS WILD-TYPE                                    12
                   vv
clus                STOMACH ADENOCARCINOMA - NOT OTHERWISE SPECIFIED (NOS)
  9P LOSS CNV                                                            6
  9P LOSS WILD-TYPE                                                     67
                   vv
clus                STOMACH INTESTINAL ADENOCARCINOMA - MUCINOUS TYPE
  9P LOSS CNV                                                       2
  9P LOSS WILD-TYPE                                                 5
                   vv
clus                STOMACH INTESTINAL ADENOCARCINOMA - PAPILLARY TYPE
  9P LOSS CNV                                                        0
  9P LOSS WILD-TYPE                                                  3
                   vv
clus                STOMACH INTESTINAL ADENOCARCINOMA - TUBULAR TYPE
  9P LOSS CNV                                                      3
  9P LOSS WILD-TYPE                                                7
                   vv
clus                STOMACH INTESTINAL ADENOCARCINOMA - TYPE NOT OTHERWISE SPECIFIED (NOS)
  9P LOSS CNV                                                                            8
  9P LOSS WILD-TYPE                                                                     20
D52V4, multiclass
                   vv
clus                T1 T2 T3 T4
  9P LOSS CNV        1 14  3  3
  9P LOSS WILD-TYPE  5 38 53 15
D52V5, multiclass
    clus
vv   9P LOSS CNV 9P LOSS WILD-TYPE
  T1           1                 5
  T2          14                38
  T3           3                53
  T4           3                15
                   vv
clus                N0 N1 N2 N3
  9P LOSS CNV        6  9  5  3
  9P LOSS WILD-TYPE 38 40 18 12
D52V6, multiclass
    clus
vv   9P LOSS CNV 9P LOSS WILD-TYPE
  N0           6                38
  N1           9                40
  N2           5                18
  N3           3                12
                   vv
clus                M0 M1 MX
  9P LOSS CNV       22  2  0
  9P LOSS WILD-TYPE 96 14  8
D52V7, multiclass
    clus
vv   9P LOSS CNV 9P LOSS WILD-TYPE
  M0          22                96
  M1           2                14
  MX           0                 8
                   vv
clus                 I II III IV
  9P LOSS CNV        4  4   7  6
  9P LOSS WILD-TYPE 20 33  32 20
D52V8, multiclass
     clus
vv    9P LOSS CNV 9P LOSS WILD-TYPE
  I             4                20
  II            4                33
  III           7                32
  IV            6                20
D52V9, binary
[1] "tbl2"
                   cls
clus                [,1] [,2]
  9P LOSS CNV          1   31
  9P LOSS WILD-TYPE    4  144
     clus
vv    9P LOSS CNV 9P LOSS WILD-TYPE
  NO            1                 4
  YES          31               144
                   vv
clus                 R0  R1  R2  RX
  9P LOSS CNV        25   1   1   3
  9P LOSS WILD-TYPE 100   6  11  22
D52V10, multiclass
    clus
vv   9P LOSS CNV 9P LOSS WILD-TYPE
  R0          25               100
  R1           1                 6
  R2           1                11
  RX           3                22
D52V11, continuous

Clustering(53) Variable = 9q loss
D53V1, survival
                   sevent
clus2                 0   1
  9Q LOSS CNV        10   1
  9Q LOSS WILD-TYPE 114  18
      9Q LOSS CNV 9Q LOSS WILD-TYPE 
               11               132 
      9Q LOSS CNV 9Q LOSS WILD-TYPE 
                1                18 
$`9Q LOSS CNV`
TCGA-BR-8291 TCGA-BR-A4J1 TCGA-CD-5799 TCGA-CG-4443 TCGA-D7-6519 TCGA-D7-6520 
        1.18         0.72         0.69        29.98        15.65         9.63 
TCGA-D7-6525 TCGA-D7-6817 TCGA-EQ-8122 TCGA-FP-8099 TCGA-FP-8631 
        5.95         4.70         7.79         1.02         0.56 

$`9Q LOSS WILD-TYPE`
TCGA-B7-5816 TCGA-B7-5818 TCGA-BR-6452 TCGA-BR-6455 TCGA-BR-6457 TCGA-BR-6458 
        5.62         0.10         0.95         1.41         1.35         1.35 
TCGA-BR-6563 TCGA-BR-6564 TCGA-BR-6565 TCGA-BR-6566 TCGA-BR-6705 TCGA-BR-6706 
        0.85         0.82         0.62         0.62         1.71         2.17 
TCGA-BR-6707 TCGA-BR-6709 TCGA-BR-6710 TCGA-BR-6801 TCGA-BR-6802 TCGA-BR-6803 
        0.99         1.22         0.66         1.12         0.76         0.66 
TCGA-BR-6852 TCGA-BR-7196 TCGA-BR-7197 TCGA-BR-7703 TCGA-BR-7704 TCGA-BR-7707 
        0.26         1.22         1.48         0.46         1.25         0.13 
TCGA-BR-7715 TCGA-BR-7716 TCGA-BR-7717 TCGA-BR-7722 TCGA-BR-7723 TCGA-BR-7851 
        1.05         0.82         0.69         0.16         4.54         0.99 
TCGA-BR-7901 TCGA-BR-7957 TCGA-BR-7958 TCGA-BR-7959 TCGA-BR-8059 TCGA-BR-8060 
        0.95         0.69         0.16         1.08         0.82         1.32 
TCGA-BR-8077 TCGA-BR-8078 TCGA-BR-8080 TCGA-BR-8081 TCGA-BR-8284 TCGA-BR-8285 
        0.69         0.95         0.49         0.46         0.72         0.26 
TCGA-BR-8286 TCGA-BR-8289 TCGA-BR-8295 TCGA-BR-8296 TCGA-BR-8297 TCGA-BR-8592 
        0.43         0.26         1.55         1.48         0.76         0.20 
TCGA-BR-A4IU TCGA-BR-A4IV TCGA-BR-A4IY TCGA-BR-A4IZ TCGA-BR-A4J2 TCGA-BR-A4J4 
        0.59         0.92         0.39         0.79         0.79         0.53 
TCGA-BR-A4J5 TCGA-BR-A4J6 TCGA-BR-A4J8 TCGA-BR-A4J9 TCGA-BR-A4PF TCGA-BR-A4QI 
        0.43         0.13         0.23         0.10         0.72         0.49 
TCGA-BR-A4QL TCGA-CD-5798 TCGA-CD-5800 TCGA-CD-5801 TCGA-CD-5802 TCGA-CD-5803 
        2.24         0.82         0.36         0.49         0.30         0.07 
TCGA-CG-4300 TCGA-CG-4301 TCGA-CG-4304 TCGA-CG-4305 TCGA-CG-4306 TCGA-CG-4436 
       20.02         3.02        27.02        15.95         1.02        52.96 
TCGA-CG-4437 TCGA-CG-4438 TCGA-CG-4440 TCGA-CG-4441 TCGA-CG-4444 TCGA-CG-4449 
        8.05        54.05         4.01        14.01        47.05        19.07 
TCGA-CG-4455 TCGA-CG-4460 TCGA-CG-4462 TCGA-CG-4465 TCGA-CG-4466 TCGA-CG-4469 
       12.03        21.99         1.02         8.98        18.94         7.07 
TCGA-CG-4472 TCGA-CG-4474 TCGA-CG-4477 TCGA-CG-5716 TCGA-CG-5717 TCGA-CG-5718 
       12.00         1.02         1.02         1.02         6.94         1.02 
TCGA-CG-5719 TCGA-CG-5720 TCGA-CG-5721 TCGA-CG-5722 TCGA-CG-5723 TCGA-CG-5724 
        1.02         0.99         5.98         0.95        70.06        12.03 
TCGA-CG-5725 TCGA-CG-5726 TCGA-CG-5727 TCGA-CG-5728 TCGA-CG-5730 TCGA-CG-5732 
       15.02        28.96        31.04        65.10         4.01        55.04 
TCGA-CG-5733 TCGA-CG-5734 TCGA-D7-5577 TCGA-D7-5578 TCGA-D7-5579 TCGA-D7-6518 
       21.07         7.99         8.65         3.58         4.54         9.80 
TCGA-D7-6521 TCGA-D7-6522 TCGA-D7-6524 TCGA-D7-6526 TCGA-D7-6527 TCGA-D7-6528 
        8.19         6.90         0.69         6.61         4.14         1.68 
TCGA-D7-6815 TCGA-D7-6818 TCGA-D7-6820 TCGA-D7-6822 TCGA-EQ-5647 TCGA-F1-6177 
        3.65         4.04         2.93         4.27         0.62         6.54 
TCGA-F1-6874 TCGA-F1-6875 TCGA-FP-7735 TCGA-FP-7829 TCGA-FP-7916 TCGA-FP-7998 
        2.01        72.23         0.39         0.20         3.02         3.58 
TCGA-FP-8209 TCGA-FP-8210 TCGA-HJ-7597 TCGA-IN-7806 TCGA-IN-7808 TCGA-IP-7968 
       59.05         5.03        26.43         6.87         3.55         2.53 

      9Q LOSS CNV 9Q LOSS WILD-TYPE 
             0.56              0.07 
      9Q LOSS CNV 9Q LOSS WILD-TYPE 
            29.98             72.23 
      9Q LOSS CNV 9Q LOSS WILD-TYPE 
            4.700             1.235 
[1] "0.6 - 30.0 (4.7)" "0.1 - 72.2 (1.2)"
       TCGA-B7-5816        TCGA-B7-5818        TCGA-BR-6452        TCGA-BR-6455 
"9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" 
       TCGA-BR-6457        TCGA-BR-6458        TCGA-BR-6563        TCGA-BR-6564 
"9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" 
       TCGA-BR-6565        TCGA-BR-6566        TCGA-BR-6705        TCGA-BR-6706 
"9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" 
       TCGA-BR-6707        TCGA-BR-6709        TCGA-BR-6710        TCGA-BR-6801 
"9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" 
       TCGA-BR-6802        TCGA-BR-6803        TCGA-BR-6852        TCGA-BR-7196 
"9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" 
       TCGA-BR-7197        TCGA-BR-7703        TCGA-BR-7704        TCGA-BR-7707 
"9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" 
       TCGA-BR-7715        TCGA-BR-7716        TCGA-BR-7717        TCGA-BR-7722 
"9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" 
       TCGA-BR-7723        TCGA-BR-7851        TCGA-BR-7901        TCGA-BR-7957 
"9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" 
       TCGA-BR-7958        TCGA-BR-7959        TCGA-BR-8059        TCGA-BR-8060 
"9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" 
       TCGA-BR-8077        TCGA-BR-8078        TCGA-BR-8080        TCGA-BR-8081 
"9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" 
       TCGA-BR-8284        TCGA-BR-8285        TCGA-BR-8286        TCGA-BR-8289 
"9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" 
       TCGA-BR-8291        TCGA-BR-8295        TCGA-BR-8296        TCGA-BR-8297 
      "9Q LOSS CNV" "9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" 
       TCGA-BR-8592        TCGA-BR-A4IU        TCGA-BR-A4IV        TCGA-BR-A4IY 
"9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" 
       TCGA-BR-A4IZ        TCGA-BR-A4J1        TCGA-BR-A4J2        TCGA-BR-A4J4 
"9Q LOSS WILD-TYPE"       "9Q LOSS CNV" "9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" 
       TCGA-BR-A4J5        TCGA-BR-A4J6        TCGA-BR-A4J8        TCGA-BR-A4J9 
"9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" 
       TCGA-BR-A4PF        TCGA-BR-A4QI        TCGA-BR-A4QL        TCGA-CD-5798 
"9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" 
       TCGA-CD-5799        TCGA-CD-5800        TCGA-CD-5801        TCGA-CD-5802 
      "9Q LOSS CNV" "9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" 
       TCGA-CD-5803        TCGA-CG-4300        TCGA-CG-4301        TCGA-CG-4304 
"9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" 
       TCGA-CG-4305        TCGA-CG-4306        TCGA-CG-4436        TCGA-CG-4437 
"9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" 
       TCGA-CG-4438        TCGA-CG-4440        TCGA-CG-4441        TCGA-CG-4443 
"9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE"       "9Q LOSS CNV" 
       TCGA-CG-4444        TCGA-CG-4449        TCGA-CG-4455        TCGA-CG-4460 
"9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" 
       TCGA-CG-4462        TCGA-CG-4465        TCGA-CG-4466        TCGA-CG-4469 
"9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" 
       TCGA-CG-4472        TCGA-CG-4474        TCGA-CG-4477        TCGA-CG-5716 
"9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" 
       TCGA-CG-5717        TCGA-CG-5718        TCGA-CG-5719        TCGA-CG-5720 
"9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" 
       TCGA-CG-5721        TCGA-CG-5722        TCGA-CG-5723        TCGA-CG-5724 
"9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" 
       TCGA-CG-5725        TCGA-CG-5726        TCGA-CG-5727        TCGA-CG-5728 
"9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" 
       TCGA-CG-5730        TCGA-CG-5732        TCGA-CG-5733        TCGA-CG-5734 
"9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" 
       TCGA-D7-5577        TCGA-D7-5578        TCGA-D7-5579        TCGA-D7-6518 
"9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" 
       TCGA-D7-6519        TCGA-D7-6520        TCGA-D7-6521        TCGA-D7-6522 
      "9Q LOSS CNV"       "9Q LOSS CNV" "9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" 
       TCGA-D7-6524        TCGA-D7-6525        TCGA-D7-6526        TCGA-D7-6527 
"9Q LOSS WILD-TYPE"       "9Q LOSS CNV" "9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" 
       TCGA-D7-6528        TCGA-D7-6815        TCGA-D7-6817        TCGA-D7-6818 
"9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE"       "9Q LOSS CNV" "9Q LOSS WILD-TYPE" 
       TCGA-D7-6820        TCGA-D7-6822        TCGA-EQ-5647        TCGA-EQ-8122 
"9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE"       "9Q LOSS CNV" 
       TCGA-F1-6177        TCGA-F1-6874        TCGA-F1-6875        TCGA-FP-7735 
"9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" 
       TCGA-FP-7829        TCGA-FP-7916        TCGA-FP-7998        TCGA-FP-8099 
"9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE"       "9Q LOSS CNV" 
       TCGA-FP-8209        TCGA-FP-8210        TCGA-FP-8631        TCGA-HJ-7597 
"9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE"       "9Q LOSS CNV" "9Q LOSS WILD-TYPE" 
       TCGA-IN-7806        TCGA-IN-7808        TCGA-IP-7968 
"9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" 
       TCGA-B7-5816        TCGA-B7-5818        TCGA-BR-6452        TCGA-BR-6455 
"9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" 
       TCGA-BR-6457        TCGA-BR-6458        TCGA-BR-6563        TCGA-BR-6564 
"9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" 
       TCGA-BR-6565        TCGA-BR-6566        TCGA-BR-6705        TCGA-BR-6706 
"9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" 
       TCGA-BR-6707        TCGA-BR-6709        TCGA-BR-6710        TCGA-BR-6801 
"9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" 
       TCGA-BR-6802        TCGA-BR-6803        TCGA-BR-6852        TCGA-BR-7196 
"9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" 
       TCGA-BR-7197        TCGA-BR-7703        TCGA-BR-7704        TCGA-BR-7707 
"9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" 
       TCGA-BR-7715        TCGA-BR-7716        TCGA-BR-7717        TCGA-BR-7722 
"9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" 
       TCGA-BR-7723        TCGA-BR-7851        TCGA-BR-7901        TCGA-BR-7957 
"9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" 
       TCGA-BR-7958        TCGA-BR-7959        TCGA-BR-8059        TCGA-BR-8060 
"9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" 
       TCGA-BR-8077        TCGA-BR-8078        TCGA-BR-8080        TCGA-BR-8081 
"9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" 
       TCGA-BR-8284        TCGA-BR-8285        TCGA-BR-8286        TCGA-BR-8289 
"9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" 
       TCGA-BR-8291        TCGA-BR-8295        TCGA-BR-8296        TCGA-BR-8297 
      "9Q LOSS CNV" "9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" 
       TCGA-BR-8592        TCGA-BR-A4IU        TCGA-BR-A4IV        TCGA-BR-A4IY 
"9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" 
       TCGA-BR-A4IZ        TCGA-BR-A4J1        TCGA-BR-A4J2        TCGA-BR-A4J4 
"9Q LOSS WILD-TYPE"       "9Q LOSS CNV" "9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" 
       TCGA-BR-A4J5        TCGA-BR-A4J6        TCGA-BR-A4J8        TCGA-BR-A4J9 
"9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" 
       TCGA-BR-A4PF        TCGA-BR-A4QI        TCGA-BR-A4QL        TCGA-CD-5798 
"9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" 
       TCGA-CD-5799        TCGA-CD-5800        TCGA-CD-5801        TCGA-CD-5802 
      "9Q LOSS CNV" "9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" 
       TCGA-CD-5803        TCGA-CG-4300        TCGA-CG-4301        TCGA-CG-4304 
"9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" 
       TCGA-CG-4305        TCGA-CG-4306        TCGA-CG-4436        TCGA-CG-4437 
"9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" 
       TCGA-CG-4438        TCGA-CG-4440        TCGA-CG-4441        TCGA-CG-4443 
"9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE"       "9Q LOSS CNV" 
       TCGA-CG-4444        TCGA-CG-4449        TCGA-CG-4455        TCGA-CG-4460 
"9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" 
       TCGA-CG-4462        TCGA-CG-4465        TCGA-CG-4466        TCGA-CG-4469 
"9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" 
       TCGA-CG-4472        TCGA-CG-4474        TCGA-CG-4477        TCGA-CG-5716 
"9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" 
       TCGA-CG-5717        TCGA-CG-5718        TCGA-CG-5719        TCGA-CG-5720 
"9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" 
       TCGA-CG-5721        TCGA-CG-5722        TCGA-CG-5723        TCGA-CG-5724 
"9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" 
       TCGA-CG-5725        TCGA-CG-5726        TCGA-CG-5727        TCGA-CG-5728 
"9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" 
       TCGA-CG-5730        TCGA-CG-5732        TCGA-CG-5733        TCGA-CG-5734 
"9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" 
       TCGA-D7-5577        TCGA-D7-5578        TCGA-D7-5579        TCGA-D7-6518 
"9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" 
       TCGA-D7-6519        TCGA-D7-6520        TCGA-D7-6521        TCGA-D7-6522 
      "9Q LOSS CNV"       "9Q LOSS CNV" "9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" 
       TCGA-D7-6524        TCGA-D7-6525        TCGA-D7-6526        TCGA-D7-6527 
"9Q LOSS WILD-TYPE"       "9Q LOSS CNV" "9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" 
       TCGA-D7-6528        TCGA-D7-6815        TCGA-D7-6817        TCGA-D7-6818 
"9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE"       "9Q LOSS CNV" "9Q LOSS WILD-TYPE" 
       TCGA-D7-6820        TCGA-D7-6822        TCGA-EQ-5647        TCGA-EQ-8122 
"9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE"       "9Q LOSS CNV" 
       TCGA-F1-6177        TCGA-F1-6874        TCGA-F1-6875        TCGA-FP-7735 
"9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" 
       TCGA-FP-7829        TCGA-FP-7916        TCGA-FP-7998        TCGA-FP-8099 
"9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE"       "9Q LOSS CNV" 
       TCGA-FP-8209        TCGA-FP-8210        TCGA-FP-8631        TCGA-HJ-7597 
"9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE"       "9Q LOSS CNV" "9Q LOSS WILD-TYPE" 
       TCGA-IN-7806        TCGA-IN-7808        TCGA-IP-7968 
"9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" 
       TCGA-B7-5816        TCGA-B7-5818        TCGA-BR-6452        TCGA-BR-6455 
"9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" 
       TCGA-BR-6457        TCGA-BR-6458        TCGA-BR-6563        TCGA-BR-6564 
"9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" 
       TCGA-BR-6565        TCGA-BR-6566        TCGA-BR-6705        TCGA-BR-6706 
"9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" 
       TCGA-BR-6707        TCGA-BR-6709        TCGA-BR-6710        TCGA-BR-6801 
"9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" 
       TCGA-BR-6802        TCGA-BR-6803        TCGA-BR-6852        TCGA-BR-7196 
"9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" 
       TCGA-BR-7197        TCGA-BR-7703        TCGA-BR-7704        TCGA-BR-7707 
"9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" 
       TCGA-BR-7715        TCGA-BR-7716        TCGA-BR-7717        TCGA-BR-7722 
"9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" 
       TCGA-BR-7723        TCGA-BR-7851        TCGA-BR-7901        TCGA-BR-7957 
"9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" 
       TCGA-BR-7958        TCGA-BR-7959        TCGA-BR-8059        TCGA-BR-8060 
"9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" 
       TCGA-BR-8077        TCGA-BR-8078        TCGA-BR-8080        TCGA-BR-8081 
"9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" 
       TCGA-BR-8284        TCGA-BR-8285        TCGA-BR-8286        TCGA-BR-8289 
"9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" 
       TCGA-BR-8291        TCGA-BR-8295        TCGA-BR-8296        TCGA-BR-8297 
      "9Q LOSS CNV" "9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" 
       TCGA-BR-8592        TCGA-BR-A4IU        TCGA-BR-A4IV        TCGA-BR-A4IY 
"9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" 
       TCGA-BR-A4IZ        TCGA-BR-A4J1        TCGA-BR-A4J2        TCGA-BR-A4J4 
"9Q LOSS WILD-TYPE"       "9Q LOSS CNV" "9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" 
       TCGA-BR-A4J5        TCGA-BR-A4J6        TCGA-BR-A4J8        TCGA-BR-A4J9 
"9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" 
       TCGA-BR-A4PF        TCGA-BR-A4QI        TCGA-BR-A4QL        TCGA-CD-5798 
"9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" 
       TCGA-CD-5799        TCGA-CD-5800        TCGA-CD-5801        TCGA-CD-5802 
      "9Q LOSS CNV" "9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" 
       TCGA-CD-5803        TCGA-CG-4300        TCGA-CG-4301        TCGA-CG-4304 
"9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" 
       TCGA-CG-4305        TCGA-CG-4306        TCGA-CG-4436        TCGA-CG-4437 
"9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" 
       TCGA-CG-4438        TCGA-CG-4440        TCGA-CG-4441        TCGA-CG-4443 
"9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE"       "9Q LOSS CNV" 
       TCGA-CG-4444        TCGA-CG-4449        TCGA-CG-4455        TCGA-CG-4460 
"9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" 
       TCGA-CG-4462        TCGA-CG-4465        TCGA-CG-4466        TCGA-CG-4469 
"9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" 
       TCGA-CG-4472        TCGA-CG-4474        TCGA-CG-4477        TCGA-CG-5716 
"9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" 
       TCGA-CG-5717        TCGA-CG-5718        TCGA-CG-5719        TCGA-CG-5720 
"9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" 
       TCGA-CG-5721        TCGA-CG-5722        TCGA-CG-5723        TCGA-CG-5724 
"9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" 
       TCGA-CG-5725        TCGA-CG-5726        TCGA-CG-5727        TCGA-CG-5728 
"9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" 
       TCGA-CG-5730        TCGA-CG-5732        TCGA-CG-5733        TCGA-CG-5734 
"9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" 
       TCGA-D7-5577        TCGA-D7-5578        TCGA-D7-5579        TCGA-D7-6518 
"9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" 
       TCGA-D7-6519        TCGA-D7-6520        TCGA-D7-6521        TCGA-D7-6522 
      "9Q LOSS CNV"       "9Q LOSS CNV" "9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" 
       TCGA-D7-6524        TCGA-D7-6525        TCGA-D7-6526        TCGA-D7-6527 
"9Q LOSS WILD-TYPE"       "9Q LOSS CNV" "9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" 
       TCGA-D7-6528        TCGA-D7-6815        TCGA-D7-6817        TCGA-D7-6818 
"9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE"       "9Q LOSS CNV" "9Q LOSS WILD-TYPE" 
       TCGA-D7-6820        TCGA-D7-6822        TCGA-EQ-5647        TCGA-EQ-8122 
"9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE"       "9Q LOSS CNV" 
       TCGA-F1-6177        TCGA-F1-6874        TCGA-F1-6875        TCGA-FP-7735 
"9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" 
       TCGA-FP-7829        TCGA-FP-7916        TCGA-FP-7998        TCGA-FP-8099 
"9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE"       "9Q LOSS CNV" 
       TCGA-FP-8209        TCGA-FP-8210        TCGA-FP-8631        TCGA-HJ-7597 
"9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE"       "9Q LOSS CNV" "9Q LOSS WILD-TYPE" 
       TCGA-IN-7806        TCGA-IN-7808        TCGA-IP-7968 
"9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" 
[1] "hr=" "1.7"
D53V2, continuous
D53V3, binary
[1] "tbl2"
                   cls
clus                [,1] [,2]
  9Q LOSS CNV          3   10
  9Q LOSS WILD-TYPE   69   98
        clus
vv       9Q LOSS CNV 9Q LOSS WILD-TYPE
  FEMALE           3                69
  MALE            10                98
                   vv
clus                STOMACH  ADENOCARCINOMA  DIFFUSE TYPE
  9Q LOSS CNV                                           1
  9Q LOSS WILD-TYPE                                     9
                   vv
clus                STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  9Q LOSS CNV                                                            2
  9Q LOSS WILD-TYPE                                                     14
                   vv
clus                STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  9Q LOSS CNV                                                                       2
  9Q LOSS WILD-TYPE                                                                 6
                   vv
clus                STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE
  9Q LOSS CNV                                                              0
  9Q LOSS WILD-TYPE                                                        3
                   vv
clus                STOMACH ADENOCARCINOMA  SIGNET RING TYPE
  9Q LOSS CNV                                              0
  9Q LOSS WILD-TYPE                                        1
                   vv
clus                STOMACH ADENOCARCINOMA - DIFFUSE TYPE
  9Q LOSS CNV                                           2
  9Q LOSS WILD-TYPE                                    14
                   vv
clus                STOMACH ADENOCARCINOMA - NOT OTHERWISE SPECIFIED (NOS)
  9Q LOSS CNV                                                            1
  9Q LOSS WILD-TYPE                                                     72
                   vv
clus                STOMACH INTESTINAL ADENOCARCINOMA - MUCINOUS TYPE
  9Q LOSS CNV                                                       1
  9Q LOSS WILD-TYPE                                                 6
                   vv
clus                STOMACH INTESTINAL ADENOCARCINOMA - PAPILLARY TYPE
  9Q LOSS CNV                                                        0
  9Q LOSS WILD-TYPE                                                  3
                   vv
clus                STOMACH INTESTINAL ADENOCARCINOMA - TUBULAR TYPE
  9Q LOSS CNV                                                      2
  9Q LOSS WILD-TYPE                                                8
                   vv
clus                STOMACH INTESTINAL ADENOCARCINOMA - TYPE NOT OTHERWISE SPECIFIED (NOS)
  9Q LOSS CNV                                                                            2
  9Q LOSS WILD-TYPE                                                                     26
D53V4, multiclass
                   vv
clus                T1 T2 T3 T4
  9Q LOSS CNV        1  6  0  0
  9Q LOSS WILD-TYPE  5 46 56 18
D53V5, multiclass
    clus
vv   9Q LOSS CNV 9Q LOSS WILD-TYPE
  T1           1                 5
  T2           6                46
  T3           0                56
  T4           0                18
                   vv
clus                N0 N1 N2 N3
  9Q LOSS CNV        1  3  2  2
  9Q LOSS WILD-TYPE 43 46 21 13
D53V6, multiclass
    clus
vv   9Q LOSS CNV 9Q LOSS WILD-TYPE
  N0           1                43
  N1           3                46
  N2           2                21
  N3           2                13
                   vv
clus                 M0  M1  MX
  9Q LOSS CNV         8   0   0
  9Q LOSS WILD-TYPE 110  16   8
D53V7, multiclass
    clus
vv   9Q LOSS CNV 9Q LOSS WILD-TYPE
  M0           8               110
  M1           0                16
  MX           0                 8
                   vv
clus                 I II III IV
  9Q LOSS CNV        1  1   4  1
  9Q LOSS WILD-TYPE 23 36  35 25
D53V8, multiclass
     clus
vv    9Q LOSS CNV 9Q LOSS WILD-TYPE
  I             1                23
  II            1                36
  III           4                35
  IV            1                25
D53V9, binary
[1] "tbl2"
                   cls
clus                [,1] [,2]
  9Q LOSS CNV          1   12
  9Q LOSS WILD-TYPE    4  163
     clus
vv    9Q LOSS CNV 9Q LOSS WILD-TYPE
  NO            1                 4
  YES          12               163
                   vv
clus                 R0  R1  R2  RX
  9Q LOSS CNV         9   1   0   1
  9Q LOSS WILD-TYPE 116   6  12  24
D53V10, multiclass
    clus
vv   9Q LOSS CNV 9Q LOSS WILD-TYPE
  R0           9               116
  R1           1                 6
  R2           0                12
  RX           1                24
D53V11, continuous

Clustering(54) Variable = 10p loss
D54V1, survival
                    sevent
clus2                  0   1
  10P LOSS CNV        10   0
  10P LOSS WILD-TYPE 114  19
      10P LOSS CNV 10P LOSS WILD-TYPE 
                10                133 
      10P LOSS CNV 10P LOSS WILD-TYPE 
                 0                 19 
$`10P LOSS CNV`
TCGA-BR-8060 TCGA-BR-A4IY TCGA-CG-4436 TCGA-CG-5732 TCGA-D7-6527 TCGA-D7-6528 
        1.32         0.39        52.96        55.04         4.14         1.68 
TCGA-D7-6820 TCGA-EQ-8122 TCGA-FP-7829 TCGA-FP-8631 
        2.93         7.79         0.20         0.56 

$`10P LOSS WILD-TYPE`
TCGA-B7-5816 TCGA-B7-5818 TCGA-BR-6452 TCGA-BR-6455 TCGA-BR-6457 TCGA-BR-6458 
        5.62         0.10         0.95         1.41         1.35         1.35 
TCGA-BR-6563 TCGA-BR-6564 TCGA-BR-6565 TCGA-BR-6566 TCGA-BR-6705 TCGA-BR-6706 
        0.85         0.82         0.62         0.62         1.71         2.17 
TCGA-BR-6707 TCGA-BR-6709 TCGA-BR-6710 TCGA-BR-6801 TCGA-BR-6802 TCGA-BR-6803 
        0.99         1.22         0.66         1.12         0.76         0.66 
TCGA-BR-6852 TCGA-BR-7196 TCGA-BR-7197 TCGA-BR-7703 TCGA-BR-7704 TCGA-BR-7707 
        0.26         1.22         1.48         0.46         1.25         0.13 
TCGA-BR-7715 TCGA-BR-7716 TCGA-BR-7717 TCGA-BR-7722 TCGA-BR-7723 TCGA-BR-7851 
        1.05         0.82         0.69         0.16         4.54         0.99 
TCGA-BR-7901 TCGA-BR-7957 TCGA-BR-7958 TCGA-BR-7959 TCGA-BR-8059 TCGA-BR-8077 
        0.95         0.69         0.16         1.08         0.82         0.69 
TCGA-BR-8078 TCGA-BR-8080 TCGA-BR-8081 TCGA-BR-8284 TCGA-BR-8285 TCGA-BR-8286 
        0.95         0.49         0.46         0.72         0.26         0.43 
TCGA-BR-8289 TCGA-BR-8291 TCGA-BR-8295 TCGA-BR-8296 TCGA-BR-8297 TCGA-BR-8592 
        0.26         1.18         1.55         1.48         0.76         0.20 
TCGA-BR-A4IU TCGA-BR-A4IV TCGA-BR-A4IZ TCGA-BR-A4J1 TCGA-BR-A4J2 TCGA-BR-A4J4 
        0.59         0.92         0.79         0.72         0.79         0.53 
TCGA-BR-A4J5 TCGA-BR-A4J6 TCGA-BR-A4J8 TCGA-BR-A4J9 TCGA-BR-A4PF TCGA-BR-A4QI 
        0.43         0.13         0.23         0.10         0.72         0.49 
TCGA-BR-A4QL TCGA-CD-5798 TCGA-CD-5799 TCGA-CD-5800 TCGA-CD-5801 TCGA-CD-5802 
        2.24         0.82         0.69         0.36         0.49         0.30 
TCGA-CD-5803 TCGA-CG-4300 TCGA-CG-4301 TCGA-CG-4304 TCGA-CG-4305 TCGA-CG-4306 
        0.07        20.02         3.02        27.02        15.95         1.02 
TCGA-CG-4437 TCGA-CG-4438 TCGA-CG-4440 TCGA-CG-4441 TCGA-CG-4443 TCGA-CG-4444 
        8.05        54.05         4.01        14.01        29.98        47.05 
TCGA-CG-4449 TCGA-CG-4455 TCGA-CG-4460 TCGA-CG-4462 TCGA-CG-4465 TCGA-CG-4466 
       19.07        12.03        21.99         1.02         8.98        18.94 
TCGA-CG-4469 TCGA-CG-4472 TCGA-CG-4474 TCGA-CG-4477 TCGA-CG-5716 TCGA-CG-5717 
        7.07        12.00         1.02         1.02         1.02         6.94 
TCGA-CG-5718 TCGA-CG-5719 TCGA-CG-5720 TCGA-CG-5721 TCGA-CG-5722 TCGA-CG-5723 
        1.02         1.02         0.99         5.98         0.95        70.06 
TCGA-CG-5724 TCGA-CG-5725 TCGA-CG-5726 TCGA-CG-5727 TCGA-CG-5728 TCGA-CG-5730 
       12.03        15.02        28.96        31.04        65.10         4.01 
TCGA-CG-5733 TCGA-CG-5734 TCGA-D7-5577 TCGA-D7-5578 TCGA-D7-5579 TCGA-D7-6518 
       21.07         7.99         8.65         3.58         4.54         9.80 
TCGA-D7-6519 TCGA-D7-6520 TCGA-D7-6521 TCGA-D7-6522 TCGA-D7-6524 TCGA-D7-6525 
       15.65         9.63         8.19         6.90         0.69         5.95 
TCGA-D7-6526 TCGA-D7-6815 TCGA-D7-6817 TCGA-D7-6818 TCGA-D7-6822 TCGA-EQ-5647 
        6.61         3.65         4.70         4.04         4.27         0.62 
TCGA-F1-6177 TCGA-F1-6874 TCGA-F1-6875 TCGA-FP-7735 TCGA-FP-7916 TCGA-FP-7998 
        6.54         2.01        72.23         0.39         3.02         3.58 
TCGA-FP-8099 TCGA-FP-8209 TCGA-FP-8210 TCGA-HJ-7597 TCGA-IN-7806 TCGA-IN-7808 
        1.02        59.05         5.03        26.43         6.87         3.55 
TCGA-IP-7968 
        2.53 

      10P LOSS CNV 10P LOSS WILD-TYPE 
              0.20               0.07 
      10P LOSS CNV 10P LOSS WILD-TYPE 
             55.04              72.23 
      10P LOSS CNV 10P LOSS WILD-TYPE 
             2.305              1.220 
[1] "0.2 - 55.0 (2.3)" "0.1 - 72.2 (1.2)"
        TCGA-B7-5816         TCGA-B7-5818         TCGA-BR-6452 
"10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" 
        TCGA-BR-6455         TCGA-BR-6457         TCGA-BR-6458 
"10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" 
        TCGA-BR-6563         TCGA-BR-6564         TCGA-BR-6565 
"10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" 
        TCGA-BR-6566         TCGA-BR-6705         TCGA-BR-6706 
"10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" 
        TCGA-BR-6707         TCGA-BR-6709         TCGA-BR-6710 
"10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" 
        TCGA-BR-6801         TCGA-BR-6802         TCGA-BR-6803 
"10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" 
        TCGA-BR-6852         TCGA-BR-7196         TCGA-BR-7197 
"10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" 
        TCGA-BR-7703         TCGA-BR-7704         TCGA-BR-7707 
"10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" 
        TCGA-BR-7715         TCGA-BR-7716         TCGA-BR-7717 
"10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" 
        TCGA-BR-7722         TCGA-BR-7723         TCGA-BR-7851 
"10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" 
        TCGA-BR-7901         TCGA-BR-7957         TCGA-BR-7958 
"10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" 
        TCGA-BR-7959         TCGA-BR-8059         TCGA-BR-8060 
"10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE"       "10P LOSS CNV" 
        TCGA-BR-8077         TCGA-BR-8078         TCGA-BR-8080 
"10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" 
        TCGA-BR-8081         TCGA-BR-8284         TCGA-BR-8285 
"10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" 
        TCGA-BR-8286         TCGA-BR-8289         TCGA-BR-8291 
"10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" 
        TCGA-BR-8295         TCGA-BR-8296         TCGA-BR-8297 
"10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" 
        TCGA-BR-8592         TCGA-BR-A4IU         TCGA-BR-A4IV 
"10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" 
        TCGA-BR-A4IY         TCGA-BR-A4IZ         TCGA-BR-A4J1 
      "10P LOSS CNV" "10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" 
        TCGA-BR-A4J2         TCGA-BR-A4J4         TCGA-BR-A4J5 
"10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" 
        TCGA-BR-A4J6         TCGA-BR-A4J8         TCGA-BR-A4J9 
"10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" 
        TCGA-BR-A4PF         TCGA-BR-A4QI         TCGA-BR-A4QL 
"10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" 
        TCGA-CD-5798         TCGA-CD-5799         TCGA-CD-5800 
"10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" 
        TCGA-CD-5801         TCGA-CD-5802         TCGA-CD-5803 
"10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" 
        TCGA-CG-4300         TCGA-CG-4301         TCGA-CG-4304 
"10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" 
        TCGA-CG-4305         TCGA-CG-4306         TCGA-CG-4436 
"10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE"       "10P LOSS CNV" 
        TCGA-CG-4437         TCGA-CG-4438         TCGA-CG-4440 
"10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" 
        TCGA-CG-4441         TCGA-CG-4443         TCGA-CG-4444 
"10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" 
        TCGA-CG-4449         TCGA-CG-4455         TCGA-CG-4460 
"10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" 
        TCGA-CG-4462         TCGA-CG-4465         TCGA-CG-4466 
"10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" 
        TCGA-CG-4469         TCGA-CG-4472         TCGA-CG-4474 
"10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" 
        TCGA-CG-4477         TCGA-CG-5716         TCGA-CG-5717 
"10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" 
        TCGA-CG-5718         TCGA-CG-5719         TCGA-CG-5720 
"10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" 
        TCGA-CG-5721         TCGA-CG-5722         TCGA-CG-5723 
"10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" 
        TCGA-CG-5724         TCGA-CG-5725         TCGA-CG-5726 
"10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" 
        TCGA-CG-5727         TCGA-CG-5728         TCGA-CG-5730 
"10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" 
        TCGA-CG-5732         TCGA-CG-5733         TCGA-CG-5734 
      "10P LOSS CNV" "10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" 
        TCGA-D7-5577         TCGA-D7-5578         TCGA-D7-5579 
"10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" 
        TCGA-D7-6518         TCGA-D7-6519         TCGA-D7-6520 
"10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" 
        TCGA-D7-6521         TCGA-D7-6522         TCGA-D7-6524 
"10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" 
        TCGA-D7-6525         TCGA-D7-6526         TCGA-D7-6527 
"10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE"       "10P LOSS CNV" 
        TCGA-D7-6528         TCGA-D7-6815         TCGA-D7-6817 
      "10P LOSS CNV" "10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" 
        TCGA-D7-6818         TCGA-D7-6820         TCGA-D7-6822 
"10P LOSS WILD-TYPE"       "10P LOSS CNV" "10P LOSS WILD-TYPE" 
        TCGA-EQ-5647         TCGA-EQ-8122         TCGA-F1-6177 
"10P LOSS WILD-TYPE"       "10P LOSS CNV" "10P LOSS WILD-TYPE" 
        TCGA-F1-6874         TCGA-F1-6875         TCGA-FP-7735 
"10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" 
        TCGA-FP-7829         TCGA-FP-7916         TCGA-FP-7998 
      "10P LOSS CNV" "10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" 
        TCGA-FP-8099         TCGA-FP-8209         TCGA-FP-8210 
"10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" 
        TCGA-FP-8631         TCGA-HJ-7597         TCGA-IN-7806 
      "10P LOSS CNV" "10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" 
        TCGA-IN-7808         TCGA-IP-7968 
"10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" 
        TCGA-B7-5816         TCGA-B7-5818         TCGA-BR-6452 
"10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" 
        TCGA-BR-6455         TCGA-BR-6457         TCGA-BR-6458 
"10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" 
        TCGA-BR-6563         TCGA-BR-6564         TCGA-BR-6565 
"10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" 
        TCGA-BR-6566         TCGA-BR-6705         TCGA-BR-6706 
"10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" 
        TCGA-BR-6707         TCGA-BR-6709         TCGA-BR-6710 
"10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" 
        TCGA-BR-6801         TCGA-BR-6802         TCGA-BR-6803 
"10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" 
        TCGA-BR-6852         TCGA-BR-7196         TCGA-BR-7197 
"10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" 
        TCGA-BR-7703         TCGA-BR-7704         TCGA-BR-7707 
"10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" 
        TCGA-BR-7715         TCGA-BR-7716         TCGA-BR-7717 
"10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" 
        TCGA-BR-7722         TCGA-BR-7723         TCGA-BR-7851 
"10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" 
        TCGA-BR-7901         TCGA-BR-7957         TCGA-BR-7958 
"10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" 
        TCGA-BR-7959         TCGA-BR-8059         TCGA-BR-8060 
"10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE"       "10P LOSS CNV" 
        TCGA-BR-8077         TCGA-BR-8078         TCGA-BR-8080 
"10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" 
        TCGA-BR-8081         TCGA-BR-8284         TCGA-BR-8285 
"10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" 
        TCGA-BR-8286         TCGA-BR-8289         TCGA-BR-8291 
"10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" 
        TCGA-BR-8295         TCGA-BR-8296         TCGA-BR-8297 
"10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" 
        TCGA-BR-8592         TCGA-BR-A4IU         TCGA-BR-A4IV 
"10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" 
        TCGA-BR-A4IY         TCGA-BR-A4IZ         TCGA-BR-A4J1 
      "10P LOSS CNV" "10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" 
        TCGA-BR-A4J2         TCGA-BR-A4J4         TCGA-BR-A4J5 
"10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" 
        TCGA-BR-A4J6         TCGA-BR-A4J8         TCGA-BR-A4J9 
"10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" 
        TCGA-BR-A4PF         TCGA-BR-A4QI         TCGA-BR-A4QL 
"10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" 
        TCGA-CD-5798         TCGA-CD-5799         TCGA-CD-5800 
"10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" 
        TCGA-CD-5801         TCGA-CD-5802         TCGA-CD-5803 
"10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" 
        TCGA-CG-4300         TCGA-CG-4301         TCGA-CG-4304 
"10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" 
        TCGA-CG-4305         TCGA-CG-4306         TCGA-CG-4436 
"10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE"       "10P LOSS CNV" 
        TCGA-CG-4437         TCGA-CG-4438         TCGA-CG-4440 
"10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" 
        TCGA-CG-4441         TCGA-CG-4443         TCGA-CG-4444 
"10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" 
        TCGA-CG-4449         TCGA-CG-4455         TCGA-CG-4460 
"10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" 
        TCGA-CG-4462         TCGA-CG-4465         TCGA-CG-4466 
"10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" 
        TCGA-CG-4469         TCGA-CG-4472         TCGA-CG-4474 
"10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" 
        TCGA-CG-4477         TCGA-CG-5716         TCGA-CG-5717 
"10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" 
        TCGA-CG-5718         TCGA-CG-5719         TCGA-CG-5720 
"10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" 
        TCGA-CG-5721         TCGA-CG-5722         TCGA-CG-5723 
"10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" 
        TCGA-CG-5724         TCGA-CG-5725         TCGA-CG-5726 
"10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" 
        TCGA-CG-5727         TCGA-CG-5728         TCGA-CG-5730 
"10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" 
        TCGA-CG-5732         TCGA-CG-5733         TCGA-CG-5734 
      "10P LOSS CNV" "10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" 
        TCGA-D7-5577         TCGA-D7-5578         TCGA-D7-5579 
"10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" 
        TCGA-D7-6518         TCGA-D7-6519         TCGA-D7-6520 
"10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" 
        TCGA-D7-6521         TCGA-D7-6522         TCGA-D7-6524 
"10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" 
        TCGA-D7-6525         TCGA-D7-6526         TCGA-D7-6527 
"10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE"       "10P LOSS CNV" 
        TCGA-D7-6528         TCGA-D7-6815         TCGA-D7-6817 
      "10P LOSS CNV" "10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" 
        TCGA-D7-6818         TCGA-D7-6820         TCGA-D7-6822 
"10P LOSS WILD-TYPE"       "10P LOSS CNV" "10P LOSS WILD-TYPE" 
        TCGA-EQ-5647         TCGA-EQ-8122         TCGA-F1-6177 
"10P LOSS WILD-TYPE"       "10P LOSS CNV" "10P LOSS WILD-TYPE" 
        TCGA-F1-6874         TCGA-F1-6875         TCGA-FP-7735 
"10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" 
        TCGA-FP-7829         TCGA-FP-7916         TCGA-FP-7998 
      "10P LOSS CNV" "10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" 
        TCGA-FP-8099         TCGA-FP-8209         TCGA-FP-8210 
"10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" 
        TCGA-FP-8631         TCGA-HJ-7597         TCGA-IN-7806 
      "10P LOSS CNV" "10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" 
        TCGA-IN-7808         TCGA-IP-7968 
"10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" 
        TCGA-B7-5816         TCGA-B7-5818         TCGA-BR-6452 
"10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" 
        TCGA-BR-6455         TCGA-BR-6457         TCGA-BR-6458 
"10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" 
        TCGA-BR-6563         TCGA-BR-6564         TCGA-BR-6565 
"10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" 
        TCGA-BR-6566         TCGA-BR-6705         TCGA-BR-6706 
"10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" 
        TCGA-BR-6707         TCGA-BR-6709         TCGA-BR-6710 
"10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" 
        TCGA-BR-6801         TCGA-BR-6802         TCGA-BR-6803 
"10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" 
        TCGA-BR-6852         TCGA-BR-7196         TCGA-BR-7197 
"10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" 
        TCGA-BR-7703         TCGA-BR-7704         TCGA-BR-7707 
"10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" 
        TCGA-BR-7715         TCGA-BR-7716         TCGA-BR-7717 
"10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" 
        TCGA-BR-7722         TCGA-BR-7723         TCGA-BR-7851 
"10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" 
        TCGA-BR-7901         TCGA-BR-7957         TCGA-BR-7958 
"10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" 
        TCGA-BR-7959         TCGA-BR-8059         TCGA-BR-8060 
"10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE"       "10P LOSS CNV" 
        TCGA-BR-8077         TCGA-BR-8078         TCGA-BR-8080 
"10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" 
        TCGA-BR-8081         TCGA-BR-8284         TCGA-BR-8285 
"10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" 
        TCGA-BR-8286         TCGA-BR-8289         TCGA-BR-8291 
"10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" 
        TCGA-BR-8295         TCGA-BR-8296         TCGA-BR-8297 
"10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" 
        TCGA-BR-8592         TCGA-BR-A4IU         TCGA-BR-A4IV 
"10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" 
        TCGA-BR-A4IY         TCGA-BR-A4IZ         TCGA-BR-A4J1 
      "10P LOSS CNV" "10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" 
        TCGA-BR-A4J2         TCGA-BR-A4J4         TCGA-BR-A4J5 
"10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" 
        TCGA-BR-A4J6         TCGA-BR-A4J8         TCGA-BR-A4J9 
"10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" 
        TCGA-BR-A4PF         TCGA-BR-A4QI         TCGA-BR-A4QL 
"10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" 
        TCGA-CD-5798         TCGA-CD-5799         TCGA-CD-5800 
"10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" 
        TCGA-CD-5801         TCGA-CD-5802         TCGA-CD-5803 
"10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" 
        TCGA-CG-4300         TCGA-CG-4301         TCGA-CG-4304 
"10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" 
        TCGA-CG-4305         TCGA-CG-4306         TCGA-CG-4436 
"10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE"       "10P LOSS CNV" 
        TCGA-CG-4437         TCGA-CG-4438         TCGA-CG-4440 
"10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" 
        TCGA-CG-4441         TCGA-CG-4443         TCGA-CG-4444 
"10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" 
        TCGA-CG-4449         TCGA-CG-4455         TCGA-CG-4460 
"10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" 
        TCGA-CG-4462         TCGA-CG-4465         TCGA-CG-4466 
"10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" 
        TCGA-CG-4469         TCGA-CG-4472         TCGA-CG-4474 
"10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" 
        TCGA-CG-4477         TCGA-CG-5716         TCGA-CG-5717 
"10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" 
        TCGA-CG-5718         TCGA-CG-5719         TCGA-CG-5720 
"10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" 
        TCGA-CG-5721         TCGA-CG-5722         TCGA-CG-5723 
"10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" 
        TCGA-CG-5724         TCGA-CG-5725         TCGA-CG-5726 
"10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" 
        TCGA-CG-5727         TCGA-CG-5728         TCGA-CG-5730 
"10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" 
        TCGA-CG-5732         TCGA-CG-5733         TCGA-CG-5734 
      "10P LOSS CNV" "10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" 
        TCGA-D7-5577         TCGA-D7-5578         TCGA-D7-5579 
"10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" 
        TCGA-D7-6518         TCGA-D7-6519         TCGA-D7-6520 
"10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" 
        TCGA-D7-6521         TCGA-D7-6522         TCGA-D7-6524 
"10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" 
        TCGA-D7-6525         TCGA-D7-6526         TCGA-D7-6527 
"10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE"       "10P LOSS CNV" 
        TCGA-D7-6528         TCGA-D7-6815         TCGA-D7-6817 
      "10P LOSS CNV" "10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" 
        TCGA-D7-6818         TCGA-D7-6820         TCGA-D7-6822 
"10P LOSS WILD-TYPE"       "10P LOSS CNV" "10P LOSS WILD-TYPE" 
        TCGA-EQ-5647         TCGA-EQ-8122         TCGA-F1-6177 
"10P LOSS WILD-TYPE"       "10P LOSS CNV" "10P LOSS WILD-TYPE" 
        TCGA-F1-6874         TCGA-F1-6875         TCGA-FP-7735 
"10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" 
        TCGA-FP-7829         TCGA-FP-7916         TCGA-FP-7998 
      "10P LOSS CNV" "10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" 
        TCGA-FP-8099         TCGA-FP-8209         TCGA-FP-8210 
"10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" 
        TCGA-FP-8631         TCGA-HJ-7597         TCGA-IN-7806 
      "10P LOSS CNV" "10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" 
        TCGA-IN-7808         TCGA-IP-7968 
"10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" 
[1] "hr="     "7.9e+07"
D54V2, continuous
D54V3, binary
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  10P LOSS CNV          4   10
  10P LOSS WILD-TYPE   68   98
        clus
vv       10P LOSS CNV 10P LOSS WILD-TYPE
  FEMALE            4                 68
  MALE             10                 98
                    vv
clus                 STOMACH  ADENOCARCINOMA  DIFFUSE TYPE
  10P LOSS CNV                                           0
  10P LOSS WILD-TYPE                                    10
                    vv
clus                 STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  10P LOSS CNV                                                            2
  10P LOSS WILD-TYPE                                                     14
                    vv
clus                 STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  10P LOSS CNV                                                                       2
  10P LOSS WILD-TYPE                                                                 6
                    vv
clus                 STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE
  10P LOSS CNV                                                              0
  10P LOSS WILD-TYPE                                                        3
                    vv
clus                 STOMACH ADENOCARCINOMA  SIGNET RING TYPE
  10P LOSS CNV                                              0
  10P LOSS WILD-TYPE                                        1
                    vv
clus                 STOMACH ADENOCARCINOMA - DIFFUSE TYPE
  10P LOSS CNV                                           0
  10P LOSS WILD-TYPE                                    16
                    vv
clus                 STOMACH ADENOCARCINOMA - NOT OTHERWISE SPECIFIED (NOS)
  10P LOSS CNV                                                            2
  10P LOSS WILD-TYPE                                                     71
                    vv
clus                 STOMACH INTESTINAL ADENOCARCINOMA - MUCINOUS TYPE
  10P LOSS CNV                                                       2
  10P LOSS WILD-TYPE                                                 5
                    vv
clus                 STOMACH INTESTINAL ADENOCARCINOMA - PAPILLARY TYPE
  10P LOSS CNV                                                        1
  10P LOSS WILD-TYPE                                                  2
                    vv
clus                 STOMACH INTESTINAL ADENOCARCINOMA - TUBULAR TYPE
  10P LOSS CNV                                                      2
  10P LOSS WILD-TYPE                                                8
                    vv
clus                 STOMACH INTESTINAL ADENOCARCINOMA - TYPE NOT OTHERWISE SPECIFIED (NOS)
  10P LOSS CNV                                                                            2
  10P LOSS WILD-TYPE                                                                     26
D54V4, multiclass
                    vv
clus                 T1 T2 T3 T4
  10P LOSS CNV        0  7  2  0
  10P LOSS WILD-TYPE  6 45 54 18
D54V5, multiclass
    clus
vv   10P LOSS CNV 10P LOSS WILD-TYPE
  T1            0                  6
  T2            7                 45
  T3            2                 54
  T4            0                 18
                    vv
clus                 N0 N1 N2 N3
  10P LOSS CNV        3  5  0  2
  10P LOSS WILD-TYPE 41 44 23 13
D54V6, multiclass
    clus
vv   10P LOSS CNV 10P LOSS WILD-TYPE
  N0            3                 41
  N1            5                 44
  N2            0                 23
  N3            2                 13
                    vv
clus                  M0  M1  MX
  10P LOSS CNV        10   0   0
  10P LOSS WILD-TYPE 108  16   8
D54V7, multiclass
    clus
vv   10P LOSS CNV 10P LOSS WILD-TYPE
  M0           10                108
  M1            0                 16
  MX            0                  8
                    vv
clus                  I II III IV
  10P LOSS CNV        3  3   1  2
  10P LOSS WILD-TYPE 21 34  38 24
D54V8, multiclass
     clus
vv    10P LOSS CNV 10P LOSS WILD-TYPE
  I              3                 21
  II             3                 34
  III            1                 38
  IV             2                 24
D54V9, binary
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  10P LOSS CNV          2   12
  10P LOSS WILD-TYPE    3  163
     clus
vv    10P LOSS CNV 10P LOSS WILD-TYPE
  NO             2                  3
  YES           12                163
                    vv
clus                  R0  R1  R2  RX
  10P LOSS CNV        10   1   0   2
  10P LOSS WILD-TYPE 115   6  12  23
D54V10, multiclass
    clus
vv   10P LOSS CNV 10P LOSS WILD-TYPE
  R0           10                115
  R1            1                  6
  R2            0                 12
  RX            2                 23
D54V11, continuous

Clustering(55) Variable = 10q loss
D55V1, survival
                    sevent
clus2                  0   1
  10Q LOSS CNV         9   0
  10Q LOSS WILD-TYPE 115  19
      10Q LOSS CNV 10Q LOSS WILD-TYPE 
                 9                134 
      10Q LOSS CNV 10Q LOSS WILD-TYPE 
                 0                 19 
$`10Q LOSS CNV`
TCGA-BR-7704 TCGA-BR-8060 TCGA-CG-4436 TCGA-CG-4466 TCGA-D7-6527 TCGA-D7-6528 
        1.25         1.32        52.96        18.94         4.14         1.68 
TCGA-D7-6817 TCGA-EQ-8122 TCGA-FP-8631 
        4.70         7.79         0.56 

$`10Q LOSS WILD-TYPE`
TCGA-B7-5816 TCGA-B7-5818 TCGA-BR-6452 TCGA-BR-6455 TCGA-BR-6457 TCGA-BR-6458 
        5.62         0.10         0.95         1.41         1.35         1.35 
TCGA-BR-6563 TCGA-BR-6564 TCGA-BR-6565 TCGA-BR-6566 TCGA-BR-6705 TCGA-BR-6706 
        0.85         0.82         0.62         0.62         1.71         2.17 
TCGA-BR-6707 TCGA-BR-6709 TCGA-BR-6710 TCGA-BR-6801 TCGA-BR-6802 TCGA-BR-6803 
        0.99         1.22         0.66         1.12         0.76         0.66 
TCGA-BR-6852 TCGA-BR-7196 TCGA-BR-7197 TCGA-BR-7703 TCGA-BR-7707 TCGA-BR-7715 
        0.26         1.22         1.48         0.46         0.13         1.05 
TCGA-BR-7716 TCGA-BR-7717 TCGA-BR-7722 TCGA-BR-7723 TCGA-BR-7851 TCGA-BR-7901 
        0.82         0.69         0.16         4.54         0.99         0.95 
TCGA-BR-7957 TCGA-BR-7958 TCGA-BR-7959 TCGA-BR-8059 TCGA-BR-8077 TCGA-BR-8078 
        0.69         0.16         1.08         0.82         0.69         0.95 
TCGA-BR-8080 TCGA-BR-8081 TCGA-BR-8284 TCGA-BR-8285 TCGA-BR-8286 TCGA-BR-8289 
        0.49         0.46         0.72         0.26         0.43         0.26 
TCGA-BR-8291 TCGA-BR-8295 TCGA-BR-8296 TCGA-BR-8297 TCGA-BR-8592 TCGA-BR-A4IU 
        1.18         1.55         1.48         0.76         0.20         0.59 
TCGA-BR-A4IV TCGA-BR-A4IY TCGA-BR-A4IZ TCGA-BR-A4J1 TCGA-BR-A4J2 TCGA-BR-A4J4 
        0.92         0.39         0.79         0.72         0.79         0.53 
TCGA-BR-A4J5 TCGA-BR-A4J6 TCGA-BR-A4J8 TCGA-BR-A4J9 TCGA-BR-A4PF TCGA-BR-A4QI 
        0.43         0.13         0.23         0.10         0.72         0.49 
TCGA-BR-A4QL TCGA-CD-5798 TCGA-CD-5799 TCGA-CD-5800 TCGA-CD-5801 TCGA-CD-5802 
        2.24         0.82         0.69         0.36         0.49         0.30 
TCGA-CD-5803 TCGA-CG-4300 TCGA-CG-4301 TCGA-CG-4304 TCGA-CG-4305 TCGA-CG-4306 
        0.07        20.02         3.02        27.02        15.95         1.02 
TCGA-CG-4437 TCGA-CG-4438 TCGA-CG-4440 TCGA-CG-4441 TCGA-CG-4443 TCGA-CG-4444 
        8.05        54.05         4.01        14.01        29.98        47.05 
TCGA-CG-4449 TCGA-CG-4455 TCGA-CG-4460 TCGA-CG-4462 TCGA-CG-4465 TCGA-CG-4469 
       19.07        12.03        21.99         1.02         8.98         7.07 
TCGA-CG-4472 TCGA-CG-4474 TCGA-CG-4477 TCGA-CG-5716 TCGA-CG-5717 TCGA-CG-5718 
       12.00         1.02         1.02         1.02         6.94         1.02 
TCGA-CG-5719 TCGA-CG-5720 TCGA-CG-5721 TCGA-CG-5722 TCGA-CG-5723 TCGA-CG-5724 
        1.02         0.99         5.98         0.95        70.06        12.03 
TCGA-CG-5725 TCGA-CG-5726 TCGA-CG-5727 TCGA-CG-5728 TCGA-CG-5730 TCGA-CG-5732 
       15.02        28.96        31.04        65.10         4.01        55.04 
TCGA-CG-5733 TCGA-CG-5734 TCGA-D7-5577 TCGA-D7-5578 TCGA-D7-5579 TCGA-D7-6518 
       21.07         7.99         8.65         3.58         4.54         9.80 
TCGA-D7-6519 TCGA-D7-6520 TCGA-D7-6521 TCGA-D7-6522 TCGA-D7-6524 TCGA-D7-6525 
       15.65         9.63         8.19         6.90         0.69         5.95 
TCGA-D7-6526 TCGA-D7-6815 TCGA-D7-6818 TCGA-D7-6820 TCGA-D7-6822 TCGA-EQ-5647 
        6.61         3.65         4.04         2.93         4.27         0.62 
TCGA-F1-6177 TCGA-F1-6874 TCGA-F1-6875 TCGA-FP-7735 TCGA-FP-7829 TCGA-FP-7916 
        6.54         2.01        72.23         0.39         0.20         3.02 
TCGA-FP-7998 TCGA-FP-8099 TCGA-FP-8209 TCGA-FP-8210 TCGA-HJ-7597 TCGA-IN-7806 
        3.58         1.02        59.05         5.03        26.43         6.87 
TCGA-IN-7808 TCGA-IP-7968 
        3.55         2.53 

      10Q LOSS CNV 10Q LOSS WILD-TYPE 
              0.56               0.07 
      10Q LOSS CNV 10Q LOSS WILD-TYPE 
             52.96              72.23 
      10Q LOSS CNV 10Q LOSS WILD-TYPE 
              4.14               1.15 
[1] "0.6 - 53.0 (4.1)" "0.1 - 72.2 (1.1)"
        TCGA-B7-5816         TCGA-B7-5818         TCGA-BR-6452 
"10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" 
        TCGA-BR-6455         TCGA-BR-6457         TCGA-BR-6458 
"10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" 
        TCGA-BR-6563         TCGA-BR-6564         TCGA-BR-6565 
"10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" 
        TCGA-BR-6566         TCGA-BR-6705         TCGA-BR-6706 
"10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" 
        TCGA-BR-6707         TCGA-BR-6709         TCGA-BR-6710 
"10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" 
        TCGA-BR-6801         TCGA-BR-6802         TCGA-BR-6803 
"10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" 
        TCGA-BR-6852         TCGA-BR-7196         TCGA-BR-7197 
"10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" 
        TCGA-BR-7703         TCGA-BR-7704         TCGA-BR-7707 
"10Q LOSS WILD-TYPE"       "10Q LOSS CNV" "10Q LOSS WILD-TYPE" 
        TCGA-BR-7715         TCGA-BR-7716         TCGA-BR-7717 
"10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" 
        TCGA-BR-7722         TCGA-BR-7723         TCGA-BR-7851 
"10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" 
        TCGA-BR-7901         TCGA-BR-7957         TCGA-BR-7958 
"10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" 
        TCGA-BR-7959         TCGA-BR-8059         TCGA-BR-8060 
"10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE"       "10Q LOSS CNV" 
        TCGA-BR-8077         TCGA-BR-8078         TCGA-BR-8080 
"10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" 
        TCGA-BR-8081         TCGA-BR-8284         TCGA-BR-8285 
"10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" 
        TCGA-BR-8286         TCGA-BR-8289         TCGA-BR-8291 
"10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" 
        TCGA-BR-8295         TCGA-BR-8296         TCGA-BR-8297 
"10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" 
        TCGA-BR-8592         TCGA-BR-A4IU         TCGA-BR-A4IV 
"10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" 
        TCGA-BR-A4IY         TCGA-BR-A4IZ         TCGA-BR-A4J1 
"10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" 
        TCGA-BR-A4J2         TCGA-BR-A4J4         TCGA-BR-A4J5 
"10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" 
        TCGA-BR-A4J6         TCGA-BR-A4J8         TCGA-BR-A4J9 
"10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" 
        TCGA-BR-A4PF         TCGA-BR-A4QI         TCGA-BR-A4QL 
"10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" 
        TCGA-CD-5798         TCGA-CD-5799         TCGA-CD-5800 
"10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" 
        TCGA-CD-5801         TCGA-CD-5802         TCGA-CD-5803 
"10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" 
        TCGA-CG-4300         TCGA-CG-4301         TCGA-CG-4304 
"10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" 
        TCGA-CG-4305         TCGA-CG-4306         TCGA-CG-4436 
"10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE"       "10Q LOSS CNV" 
        TCGA-CG-4437         TCGA-CG-4438         TCGA-CG-4440 
"10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" 
        TCGA-CG-4441         TCGA-CG-4443         TCGA-CG-4444 
"10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" 
        TCGA-CG-4449         TCGA-CG-4455         TCGA-CG-4460 
"10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" 
        TCGA-CG-4462         TCGA-CG-4465         TCGA-CG-4466 
"10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE"       "10Q LOSS CNV" 
        TCGA-CG-4469         TCGA-CG-4472         TCGA-CG-4474 
"10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" 
        TCGA-CG-4477         TCGA-CG-5716         TCGA-CG-5717 
"10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" 
        TCGA-CG-5718         TCGA-CG-5719         TCGA-CG-5720 
"10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" 
        TCGA-CG-5721         TCGA-CG-5722         TCGA-CG-5723 
"10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" 
        TCGA-CG-5724         TCGA-CG-5725         TCGA-CG-5726 
"10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" 
        TCGA-CG-5727         TCGA-CG-5728         TCGA-CG-5730 
"10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" 
        TCGA-CG-5732         TCGA-CG-5733         TCGA-CG-5734 
"10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" 
        TCGA-D7-5577         TCGA-D7-5578         TCGA-D7-5579 
"10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" 
        TCGA-D7-6518         TCGA-D7-6519         TCGA-D7-6520 
"10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" 
        TCGA-D7-6521         TCGA-D7-6522         TCGA-D7-6524 
"10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" 
        TCGA-D7-6525         TCGA-D7-6526         TCGA-D7-6527 
"10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE"       "10Q LOSS CNV" 
        TCGA-D7-6528         TCGA-D7-6815         TCGA-D7-6817 
      "10Q LOSS CNV" "10Q LOSS WILD-TYPE"       "10Q LOSS CNV" 
        TCGA-D7-6818         TCGA-D7-6820         TCGA-D7-6822 
"10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" 
        TCGA-EQ-5647         TCGA-EQ-8122         TCGA-F1-6177 
"10Q LOSS WILD-TYPE"       "10Q LOSS CNV" "10Q LOSS WILD-TYPE" 
        TCGA-F1-6874         TCGA-F1-6875         TCGA-FP-7735 
"10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" 
        TCGA-FP-7829         TCGA-FP-7916         TCGA-FP-7998 
"10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" 
        TCGA-FP-8099         TCGA-FP-8209         TCGA-FP-8210 
"10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" 
        TCGA-FP-8631         TCGA-HJ-7597         TCGA-IN-7806 
      "10Q LOSS CNV" "10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" 
        TCGA-IN-7808         TCGA-IP-7968 
"10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" 
        TCGA-B7-5816         TCGA-B7-5818         TCGA-BR-6452 
"10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" 
        TCGA-BR-6455         TCGA-BR-6457         TCGA-BR-6458 
"10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" 
        TCGA-BR-6563         TCGA-BR-6564         TCGA-BR-6565 
"10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" 
        TCGA-BR-6566         TCGA-BR-6705         TCGA-BR-6706 
"10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" 
        TCGA-BR-6707         TCGA-BR-6709         TCGA-BR-6710 
"10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" 
        TCGA-BR-6801         TCGA-BR-6802         TCGA-BR-6803 
"10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" 
        TCGA-BR-6852         TCGA-BR-7196         TCGA-BR-7197 
"10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" 
        TCGA-BR-7703         TCGA-BR-7704         TCGA-BR-7707 
"10Q LOSS WILD-TYPE"       "10Q LOSS CNV" "10Q LOSS WILD-TYPE" 
        TCGA-BR-7715         TCGA-BR-7716         TCGA-BR-7717 
"10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" 
        TCGA-BR-7722         TCGA-BR-7723         TCGA-BR-7851 
"10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" 
        TCGA-BR-7901         TCGA-BR-7957         TCGA-BR-7958 
"10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" 
        TCGA-BR-7959         TCGA-BR-8059         TCGA-BR-8060 
"10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE"       "10Q LOSS CNV" 
        TCGA-BR-8077         TCGA-BR-8078         TCGA-BR-8080 
"10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" 
        TCGA-BR-8081         TCGA-BR-8284         TCGA-BR-8285 
"10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" 
        TCGA-BR-8286         TCGA-BR-8289         TCGA-BR-8291 
"10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" 
        TCGA-BR-8295         TCGA-BR-8296         TCGA-BR-8297 
"10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" 
        TCGA-BR-8592         TCGA-BR-A4IU         TCGA-BR-A4IV 
"10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" 
        TCGA-BR-A4IY         TCGA-BR-A4IZ         TCGA-BR-A4J1 
"10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" 
        TCGA-BR-A4J2         TCGA-BR-A4J4         TCGA-BR-A4J5 
"10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" 
        TCGA-BR-A4J6         TCGA-BR-A4J8         TCGA-BR-A4J9 
"10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" 
        TCGA-BR-A4PF         TCGA-BR-A4QI         TCGA-BR-A4QL 
"10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" 
        TCGA-CD-5798         TCGA-CD-5799         TCGA-CD-5800 
"10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" 
        TCGA-CD-5801         TCGA-CD-5802         TCGA-CD-5803 
"10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" 
        TCGA-CG-4300         TCGA-CG-4301         TCGA-CG-4304 
"10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" 
        TCGA-CG-4305         TCGA-CG-4306         TCGA-CG-4436 
"10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE"       "10Q LOSS CNV" 
        TCGA-CG-4437         TCGA-CG-4438         TCGA-CG-4440 
"10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" 
        TCGA-CG-4441         TCGA-CG-4443         TCGA-CG-4444 
"10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" 
        TCGA-CG-4449         TCGA-CG-4455         TCGA-CG-4460 
"10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" 
        TCGA-CG-4462         TCGA-CG-4465         TCGA-CG-4466 
"10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE"       "10Q LOSS CNV" 
        TCGA-CG-4469         TCGA-CG-4472         TCGA-CG-4474 
"10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" 
        TCGA-CG-4477         TCGA-CG-5716         TCGA-CG-5717 
"10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" 
        TCGA-CG-5718         TCGA-CG-5719         TCGA-CG-5720 
"10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" 
        TCGA-CG-5721         TCGA-CG-5722         TCGA-CG-5723 
"10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" 
        TCGA-CG-5724         TCGA-CG-5725         TCGA-CG-5726 
"10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" 
        TCGA-CG-5727         TCGA-CG-5728         TCGA-CG-5730 
"10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" 
        TCGA-CG-5732         TCGA-CG-5733         TCGA-CG-5734 
"10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" 
        TCGA-D7-5577         TCGA-D7-5578         TCGA-D7-5579 
"10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" 
        TCGA-D7-6518         TCGA-D7-6519         TCGA-D7-6520 
"10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" 
        TCGA-D7-6521         TCGA-D7-6522         TCGA-D7-6524 
"10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" 
        TCGA-D7-6525         TCGA-D7-6526         TCGA-D7-6527 
"10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE"       "10Q LOSS CNV" 
        TCGA-D7-6528         TCGA-D7-6815         TCGA-D7-6817 
      "10Q LOSS CNV" "10Q LOSS WILD-TYPE"       "10Q LOSS CNV" 
        TCGA-D7-6818         TCGA-D7-6820         TCGA-D7-6822 
"10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" 
        TCGA-EQ-5647         TCGA-EQ-8122         TCGA-F1-6177 
"10Q LOSS WILD-TYPE"       "10Q LOSS CNV" "10Q LOSS WILD-TYPE" 
        TCGA-F1-6874         TCGA-F1-6875         TCGA-FP-7735 
"10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" 
        TCGA-FP-7829         TCGA-FP-7916         TCGA-FP-7998 
"10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" 
        TCGA-FP-8099         TCGA-FP-8209         TCGA-FP-8210 
"10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" 
        TCGA-FP-8631         TCGA-HJ-7597         TCGA-IN-7806 
      "10Q LOSS CNV" "10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" 
        TCGA-IN-7808         TCGA-IP-7968 
"10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" 
        TCGA-B7-5816         TCGA-B7-5818         TCGA-BR-6452 
"10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" 
        TCGA-BR-6455         TCGA-BR-6457         TCGA-BR-6458 
"10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" 
        TCGA-BR-6563         TCGA-BR-6564         TCGA-BR-6565 
"10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" 
        TCGA-BR-6566         TCGA-BR-6705         TCGA-BR-6706 
"10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" 
        TCGA-BR-6707         TCGA-BR-6709         TCGA-BR-6710 
"10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" 
        TCGA-BR-6801         TCGA-BR-6802         TCGA-BR-6803 
"10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" 
        TCGA-BR-6852         TCGA-BR-7196         TCGA-BR-7197 
"10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" 
        TCGA-BR-7703         TCGA-BR-7704         TCGA-BR-7707 
"10Q LOSS WILD-TYPE"       "10Q LOSS CNV" "10Q LOSS WILD-TYPE" 
        TCGA-BR-7715         TCGA-BR-7716         TCGA-BR-7717 
"10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" 
        TCGA-BR-7722         TCGA-BR-7723         TCGA-BR-7851 
"10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" 
        TCGA-BR-7901         TCGA-BR-7957         TCGA-BR-7958 
"10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" 
        TCGA-BR-7959         TCGA-BR-8059         TCGA-BR-8060 
"10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE"       "10Q LOSS CNV" 
        TCGA-BR-8077         TCGA-BR-8078         TCGA-BR-8080 
"10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" 
        TCGA-BR-8081         TCGA-BR-8284         TCGA-BR-8285 
"10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" 
        TCGA-BR-8286         TCGA-BR-8289         TCGA-BR-8291 
"10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" 
        TCGA-BR-8295         TCGA-BR-8296         TCGA-BR-8297 
"10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" 
        TCGA-BR-8592         TCGA-BR-A4IU         TCGA-BR-A4IV 
"10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" 
        TCGA-BR-A4IY         TCGA-BR-A4IZ         TCGA-BR-A4J1 
"10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" 
        TCGA-BR-A4J2         TCGA-BR-A4J4         TCGA-BR-A4J5 
"10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" 
        TCGA-BR-A4J6         TCGA-BR-A4J8         TCGA-BR-A4J9 
"10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" 
        TCGA-BR-A4PF         TCGA-BR-A4QI         TCGA-BR-A4QL 
"10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" 
        TCGA-CD-5798         TCGA-CD-5799         TCGA-CD-5800 
"10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" 
        TCGA-CD-5801         TCGA-CD-5802         TCGA-CD-5803 
"10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" 
        TCGA-CG-4300         TCGA-CG-4301         TCGA-CG-4304 
"10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" 
        TCGA-CG-4305         TCGA-CG-4306         TCGA-CG-4436 
"10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE"       "10Q LOSS CNV" 
        TCGA-CG-4437         TCGA-CG-4438         TCGA-CG-4440 
"10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" 
        TCGA-CG-4441         TCGA-CG-4443         TCGA-CG-4444 
"10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" 
        TCGA-CG-4449         TCGA-CG-4455         TCGA-CG-4460 
"10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" 
        TCGA-CG-4462         TCGA-CG-4465         TCGA-CG-4466 
"10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE"       "10Q LOSS CNV" 
        TCGA-CG-4469         TCGA-CG-4472         TCGA-CG-4474 
"10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" 
        TCGA-CG-4477         TCGA-CG-5716         TCGA-CG-5717 
"10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" 
        TCGA-CG-5718         TCGA-CG-5719         TCGA-CG-5720 
"10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" 
        TCGA-CG-5721         TCGA-CG-5722         TCGA-CG-5723 
"10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" 
        TCGA-CG-5724         TCGA-CG-5725         TCGA-CG-5726 
"10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" 
        TCGA-CG-5727         TCGA-CG-5728         TCGA-CG-5730 
"10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" 
        TCGA-CG-5732         TCGA-CG-5733         TCGA-CG-5734 
"10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" 
        TCGA-D7-5577         TCGA-D7-5578         TCGA-D7-5579 
"10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" 
        TCGA-D7-6518         TCGA-D7-6519         TCGA-D7-6520 
"10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" 
        TCGA-D7-6521         TCGA-D7-6522         TCGA-D7-6524 
"10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" 
        TCGA-D7-6525         TCGA-D7-6526         TCGA-D7-6527 
"10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE"       "10Q LOSS CNV" 
        TCGA-D7-6528         TCGA-D7-6815         TCGA-D7-6817 
      "10Q LOSS CNV" "10Q LOSS WILD-TYPE"       "10Q LOSS CNV" 
        TCGA-D7-6818         TCGA-D7-6820         TCGA-D7-6822 
"10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" 
        TCGA-EQ-5647         TCGA-EQ-8122         TCGA-F1-6177 
"10Q LOSS WILD-TYPE"       "10Q LOSS CNV" "10Q LOSS WILD-TYPE" 
        TCGA-F1-6874         TCGA-F1-6875         TCGA-FP-7735 
"10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" 
        TCGA-FP-7829         TCGA-FP-7916         TCGA-FP-7998 
"10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" 
        TCGA-FP-8099         TCGA-FP-8209         TCGA-FP-8210 
"10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" 
        TCGA-FP-8631         TCGA-HJ-7597         TCGA-IN-7806 
      "10Q LOSS CNV" "10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" 
        TCGA-IN-7808         TCGA-IP-7968 
"10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" 
[1] "hr="     "7.5e+07"
D55V2, continuous
D55V3, binary
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  10Q LOSS CNV          5    6
  10Q LOSS WILD-TYPE   67  102
        clus
vv       10Q LOSS CNV 10Q LOSS WILD-TYPE
  FEMALE            5                 67
  MALE              6                102
                    vv
clus                 STOMACH  ADENOCARCINOMA  DIFFUSE TYPE
  10Q LOSS CNV                                           0
  10Q LOSS WILD-TYPE                                    10
                    vv
clus                 STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  10Q LOSS CNV                                                            1
  10Q LOSS WILD-TYPE                                                     15
                    vv
clus                 STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  10Q LOSS CNV                                                                       2
  10Q LOSS WILD-TYPE                                                                 6
                    vv
clus                 STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE
  10Q LOSS CNV                                                              0
  10Q LOSS WILD-TYPE                                                        3
                    vv
clus                 STOMACH ADENOCARCINOMA  SIGNET RING TYPE
  10Q LOSS CNV                                              0
  10Q LOSS WILD-TYPE                                        1
                    vv
clus                 STOMACH ADENOCARCINOMA - DIFFUSE TYPE
  10Q LOSS CNV                                           0
  10Q LOSS WILD-TYPE                                    16
                    vv
clus                 STOMACH ADENOCARCINOMA - NOT OTHERWISE SPECIFIED (NOS)
  10Q LOSS CNV                                                            1
  10Q LOSS WILD-TYPE                                                     72
                    vv
clus                 STOMACH INTESTINAL ADENOCARCINOMA - MUCINOUS TYPE
  10Q LOSS CNV                                                       0
  10Q LOSS WILD-TYPE                                                 7
                    vv
clus                 STOMACH INTESTINAL ADENOCARCINOMA - PAPILLARY TYPE
  10Q LOSS CNV                                                        1
  10Q LOSS WILD-TYPE                                                  2
                    vv
clus                 STOMACH INTESTINAL ADENOCARCINOMA - TUBULAR TYPE
  10Q LOSS CNV                                                      2
  10Q LOSS WILD-TYPE                                                8
                    vv
clus                 STOMACH INTESTINAL ADENOCARCINOMA - TYPE NOT OTHERWISE SPECIFIED (NOS)
  10Q LOSS CNV                                                                            3
  10Q LOSS WILD-TYPE                                                                     25
D55V4, multiclass
                    vv
clus                 T1 T2 T3 T4
  10Q LOSS CNV        0  5  2  0
  10Q LOSS WILD-TYPE  6 47 54 18
D55V5, multiclass
    clus
vv   10Q LOSS CNV 10Q LOSS WILD-TYPE
  T1            0                  6
  T2            5                 47
  T3            2                 54
  T4            0                 18
                    vv
clus                 N0 N1 N2 N3
  10Q LOSS CNV        4  3  0  1
  10Q LOSS WILD-TYPE 40 46 23 14
D55V6, multiclass
    clus
vv   10Q LOSS CNV 10Q LOSS WILD-TYPE
  N0            4                 40
  N1            3                 46
  N2            0                 23
  N3            1                 14
                    vv
clus                  M0  M1  MX
  10Q LOSS CNV         8   0   0
  10Q LOSS WILD-TYPE 110  16   8
D55V7, multiclass
    clus
vv   10Q LOSS CNV 10Q LOSS WILD-TYPE
  M0            8                110
  M1            0                 16
  MX            0                  8
                    vv
clus                  I II III IV
  10Q LOSS CNV        3  3   1  0
  10Q LOSS WILD-TYPE 21 34  38 26
D55V8, multiclass
     clus
vv    10Q LOSS CNV 10Q LOSS WILD-TYPE
  I              3                 21
  II             3                 34
  III            1                 38
  IV             0                 26
D55V9, binary
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  10Q LOSS CNV          1   10
  10Q LOSS WILD-TYPE    4  165
     clus
vv    10Q LOSS CNV 10Q LOSS WILD-TYPE
  NO             1                  4
  YES           10                165
                    vv
clus                  R0  R1  R2  RX
  10Q LOSS CNV         9   0   0   1
  10Q LOSS WILD-TYPE 116   7  12  24
D55V10, multiclass
    clus
vv   10Q LOSS CNV 10Q LOSS WILD-TYPE
  R0            9                116
  R1            0                  7
  R2            0                 12
  RX            1                 24
D55V11, continuous

Clustering(56) Variable = 11p loss
D56V1, survival
                    sevent
clus2                  0   1
  11P LOSS CNV         7   3
  11P LOSS WILD-TYPE 117  16
      11P LOSS CNV 11P LOSS WILD-TYPE 
                10                133 
      11P LOSS CNV 11P LOSS WILD-TYPE 
                 3                 16 
$`11P LOSS CNV`
TCGA-BR-A4J1 TCGA-CD-5799 TCGA-CD-5802 TCGA-CG-4443 TCGA-CG-4460 TCGA-CG-4477 
        0.72         0.69         0.30        29.98        21.99         1.02 
TCGA-CG-5724 TCGA-CG-5730 TCGA-D7-6519 TCGA-D7-6815 
       12.03         4.01        15.65         3.65 

$`11P LOSS WILD-TYPE`
TCGA-B7-5816 TCGA-B7-5818 TCGA-BR-6452 TCGA-BR-6455 TCGA-BR-6457 TCGA-BR-6458 
        5.62         0.10         0.95         1.41         1.35         1.35 
TCGA-BR-6563 TCGA-BR-6564 TCGA-BR-6565 TCGA-BR-6566 TCGA-BR-6705 TCGA-BR-6706 
        0.85         0.82         0.62         0.62         1.71         2.17 
TCGA-BR-6707 TCGA-BR-6709 TCGA-BR-6710 TCGA-BR-6801 TCGA-BR-6802 TCGA-BR-6803 
        0.99         1.22         0.66         1.12         0.76         0.66 
TCGA-BR-6852 TCGA-BR-7196 TCGA-BR-7197 TCGA-BR-7703 TCGA-BR-7704 TCGA-BR-7707 
        0.26         1.22         1.48         0.46         1.25         0.13 
TCGA-BR-7715 TCGA-BR-7716 TCGA-BR-7717 TCGA-BR-7722 TCGA-BR-7723 TCGA-BR-7851 
        1.05         0.82         0.69         0.16         4.54         0.99 
TCGA-BR-7901 TCGA-BR-7957 TCGA-BR-7958 TCGA-BR-7959 TCGA-BR-8059 TCGA-BR-8060 
        0.95         0.69         0.16         1.08         0.82         1.32 
TCGA-BR-8077 TCGA-BR-8078 TCGA-BR-8080 TCGA-BR-8081 TCGA-BR-8284 TCGA-BR-8285 
        0.69         0.95         0.49         0.46         0.72         0.26 
TCGA-BR-8286 TCGA-BR-8289 TCGA-BR-8291 TCGA-BR-8295 TCGA-BR-8296 TCGA-BR-8297 
        0.43         0.26         1.18         1.55         1.48         0.76 
TCGA-BR-8592 TCGA-BR-A4IU TCGA-BR-A4IV TCGA-BR-A4IY TCGA-BR-A4IZ TCGA-BR-A4J2 
        0.20         0.59         0.92         0.39         0.79         0.79 
TCGA-BR-A4J4 TCGA-BR-A4J5 TCGA-BR-A4J6 TCGA-BR-A4J8 TCGA-BR-A4J9 TCGA-BR-A4PF 
        0.53         0.43         0.13         0.23         0.10         0.72 
TCGA-BR-A4QI TCGA-BR-A4QL TCGA-CD-5798 TCGA-CD-5800 TCGA-CD-5801 TCGA-CD-5803 
        0.49         2.24         0.82         0.36         0.49         0.07 
TCGA-CG-4300 TCGA-CG-4301 TCGA-CG-4304 TCGA-CG-4305 TCGA-CG-4306 TCGA-CG-4436 
       20.02         3.02        27.02        15.95         1.02        52.96 
TCGA-CG-4437 TCGA-CG-4438 TCGA-CG-4440 TCGA-CG-4441 TCGA-CG-4444 TCGA-CG-4449 
        8.05        54.05         4.01        14.01        47.05        19.07 
TCGA-CG-4455 TCGA-CG-4462 TCGA-CG-4465 TCGA-CG-4466 TCGA-CG-4469 TCGA-CG-4472 
       12.03         1.02         8.98        18.94         7.07        12.00 
TCGA-CG-4474 TCGA-CG-5716 TCGA-CG-5717 TCGA-CG-5718 TCGA-CG-5719 TCGA-CG-5720 
        1.02         1.02         6.94         1.02         1.02         0.99 
TCGA-CG-5721 TCGA-CG-5722 TCGA-CG-5723 TCGA-CG-5725 TCGA-CG-5726 TCGA-CG-5727 
        5.98         0.95        70.06        15.02        28.96        31.04 
TCGA-CG-5728 TCGA-CG-5732 TCGA-CG-5733 TCGA-CG-5734 TCGA-D7-5577 TCGA-D7-5578 
       65.10        55.04        21.07         7.99         8.65         3.58 
TCGA-D7-5579 TCGA-D7-6518 TCGA-D7-6520 TCGA-D7-6521 TCGA-D7-6522 TCGA-D7-6524 
        4.54         9.80         9.63         8.19         6.90         0.69 
TCGA-D7-6525 TCGA-D7-6526 TCGA-D7-6527 TCGA-D7-6528 TCGA-D7-6817 TCGA-D7-6818 
        5.95         6.61         4.14         1.68         4.70         4.04 
TCGA-D7-6820 TCGA-D7-6822 TCGA-EQ-5647 TCGA-EQ-8122 TCGA-F1-6177 TCGA-F1-6874 
        2.93         4.27         0.62         7.79         6.54         2.01 
TCGA-F1-6875 TCGA-FP-7735 TCGA-FP-7829 TCGA-FP-7916 TCGA-FP-7998 TCGA-FP-8099 
       72.23         0.39         0.20         3.02         3.58         1.02 
TCGA-FP-8209 TCGA-FP-8210 TCGA-FP-8631 TCGA-HJ-7597 TCGA-IN-7806 TCGA-IN-7808 
       59.05         5.03         0.56        26.43         6.87         3.55 
TCGA-IP-7968 
        2.53 

      11P LOSS CNV 11P LOSS WILD-TYPE 
              0.30               0.07 
      11P LOSS CNV 11P LOSS WILD-TYPE 
             29.98              72.23 
      11P LOSS CNV 11P LOSS WILD-TYPE 
              3.83               1.22 
[1] "0.3 - 30.0 (3.8)" "0.1 - 72.2 (1.2)"
        TCGA-B7-5816         TCGA-B7-5818         TCGA-BR-6452 
"11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" 
        TCGA-BR-6455         TCGA-BR-6457         TCGA-BR-6458 
"11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" 
        TCGA-BR-6563         TCGA-BR-6564         TCGA-BR-6565 
"11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" 
        TCGA-BR-6566         TCGA-BR-6705         TCGA-BR-6706 
"11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" 
        TCGA-BR-6707         TCGA-BR-6709         TCGA-BR-6710 
"11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" 
        TCGA-BR-6801         TCGA-BR-6802         TCGA-BR-6803 
"11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" 
        TCGA-BR-6852         TCGA-BR-7196         TCGA-BR-7197 
"11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" 
        TCGA-BR-7703         TCGA-BR-7704         TCGA-BR-7707 
"11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" 
        TCGA-BR-7715         TCGA-BR-7716         TCGA-BR-7717 
"11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" 
        TCGA-BR-7722         TCGA-BR-7723         TCGA-BR-7851 
"11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" 
        TCGA-BR-7901         TCGA-BR-7957         TCGA-BR-7958 
"11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" 
        TCGA-BR-7959         TCGA-BR-8059         TCGA-BR-8060 
"11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" 
        TCGA-BR-8077         TCGA-BR-8078         TCGA-BR-8080 
"11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" 
        TCGA-BR-8081         TCGA-BR-8284         TCGA-BR-8285 
"11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" 
        TCGA-BR-8286         TCGA-BR-8289         TCGA-BR-8291 
"11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" 
        TCGA-BR-8295         TCGA-BR-8296         TCGA-BR-8297 
"11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" 
        TCGA-BR-8592         TCGA-BR-A4IU         TCGA-BR-A4IV 
"11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" 
        TCGA-BR-A4IY         TCGA-BR-A4IZ         TCGA-BR-A4J1 
"11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE"       "11P LOSS CNV" 
        TCGA-BR-A4J2         TCGA-BR-A4J4         TCGA-BR-A4J5 
"11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" 
        TCGA-BR-A4J6         TCGA-BR-A4J8         TCGA-BR-A4J9 
"11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" 
        TCGA-BR-A4PF         TCGA-BR-A4QI         TCGA-BR-A4QL 
"11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" 
        TCGA-CD-5798         TCGA-CD-5799         TCGA-CD-5800 
"11P LOSS WILD-TYPE"       "11P LOSS CNV" "11P LOSS WILD-TYPE" 
        TCGA-CD-5801         TCGA-CD-5802         TCGA-CD-5803 
"11P LOSS WILD-TYPE"       "11P LOSS CNV" "11P LOSS WILD-TYPE" 
        TCGA-CG-4300         TCGA-CG-4301         TCGA-CG-4304 
"11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" 
        TCGA-CG-4305         TCGA-CG-4306         TCGA-CG-4436 
"11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" 
        TCGA-CG-4437         TCGA-CG-4438         TCGA-CG-4440 
"11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" 
        TCGA-CG-4441         TCGA-CG-4443         TCGA-CG-4444 
"11P LOSS WILD-TYPE"       "11P LOSS CNV" "11P LOSS WILD-TYPE" 
        TCGA-CG-4449         TCGA-CG-4455         TCGA-CG-4460 
"11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE"       "11P LOSS CNV" 
        TCGA-CG-4462         TCGA-CG-4465         TCGA-CG-4466 
"11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" 
        TCGA-CG-4469         TCGA-CG-4472         TCGA-CG-4474 
"11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" 
        TCGA-CG-4477         TCGA-CG-5716         TCGA-CG-5717 
      "11P LOSS CNV" "11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" 
        TCGA-CG-5718         TCGA-CG-5719         TCGA-CG-5720 
"11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" 
        TCGA-CG-5721         TCGA-CG-5722         TCGA-CG-5723 
"11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" 
        TCGA-CG-5724         TCGA-CG-5725         TCGA-CG-5726 
      "11P LOSS CNV" "11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" 
        TCGA-CG-5727         TCGA-CG-5728         TCGA-CG-5730 
"11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE"       "11P LOSS CNV" 
        TCGA-CG-5732         TCGA-CG-5733         TCGA-CG-5734 
"11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" 
        TCGA-D7-5577         TCGA-D7-5578         TCGA-D7-5579 
"11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" 
        TCGA-D7-6518         TCGA-D7-6519         TCGA-D7-6520 
"11P LOSS WILD-TYPE"       "11P LOSS CNV" "11P LOSS WILD-TYPE" 
        TCGA-D7-6521         TCGA-D7-6522         TCGA-D7-6524 
"11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" 
        TCGA-D7-6525         TCGA-D7-6526         TCGA-D7-6527 
"11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" 
        TCGA-D7-6528         TCGA-D7-6815         TCGA-D7-6817 
"11P LOSS WILD-TYPE"       "11P LOSS CNV" "11P LOSS WILD-TYPE" 
        TCGA-D7-6818         TCGA-D7-6820         TCGA-D7-6822 
"11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" 
        TCGA-EQ-5647         TCGA-EQ-8122         TCGA-F1-6177 
"11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" 
        TCGA-F1-6874         TCGA-F1-6875         TCGA-FP-7735 
"11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" 
        TCGA-FP-7829         TCGA-FP-7916         TCGA-FP-7998 
"11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" 
        TCGA-FP-8099         TCGA-FP-8209         TCGA-FP-8210 
"11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" 
        TCGA-FP-8631         TCGA-HJ-7597         TCGA-IN-7806 
"11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" 
        TCGA-IN-7808         TCGA-IP-7968 
"11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" 
        TCGA-B7-5816         TCGA-B7-5818         TCGA-BR-6452 
"11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" 
        TCGA-BR-6455         TCGA-BR-6457         TCGA-BR-6458 
"11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" 
        TCGA-BR-6563         TCGA-BR-6564         TCGA-BR-6565 
"11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" 
        TCGA-BR-6566         TCGA-BR-6705         TCGA-BR-6706 
"11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" 
        TCGA-BR-6707         TCGA-BR-6709         TCGA-BR-6710 
"11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" 
        TCGA-BR-6801         TCGA-BR-6802         TCGA-BR-6803 
"11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" 
        TCGA-BR-6852         TCGA-BR-7196         TCGA-BR-7197 
"11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" 
        TCGA-BR-7703         TCGA-BR-7704         TCGA-BR-7707 
"11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" 
        TCGA-BR-7715         TCGA-BR-7716         TCGA-BR-7717 
"11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" 
        TCGA-BR-7722         TCGA-BR-7723         TCGA-BR-7851 
"11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" 
        TCGA-BR-7901         TCGA-BR-7957         TCGA-BR-7958 
"11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" 
        TCGA-BR-7959         TCGA-BR-8059         TCGA-BR-8060 
"11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" 
        TCGA-BR-8077         TCGA-BR-8078         TCGA-BR-8080 
"11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" 
        TCGA-BR-8081         TCGA-BR-8284         TCGA-BR-8285 
"11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" 
        TCGA-BR-8286         TCGA-BR-8289         TCGA-BR-8291 
"11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" 
        TCGA-BR-8295         TCGA-BR-8296         TCGA-BR-8297 
"11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" 
        TCGA-BR-8592         TCGA-BR-A4IU         TCGA-BR-A4IV 
"11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" 
        TCGA-BR-A4IY         TCGA-BR-A4IZ         TCGA-BR-A4J1 
"11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE"       "11P LOSS CNV" 
        TCGA-BR-A4J2         TCGA-BR-A4J4         TCGA-BR-A4J5 
"11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" 
        TCGA-BR-A4J6         TCGA-BR-A4J8         TCGA-BR-A4J9 
"11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" 
        TCGA-BR-A4PF         TCGA-BR-A4QI         TCGA-BR-A4QL 
"11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" 
        TCGA-CD-5798         TCGA-CD-5799         TCGA-CD-5800 
"11P LOSS WILD-TYPE"       "11P LOSS CNV" "11P LOSS WILD-TYPE" 
        TCGA-CD-5801         TCGA-CD-5802         TCGA-CD-5803 
"11P LOSS WILD-TYPE"       "11P LOSS CNV" "11P LOSS WILD-TYPE" 
        TCGA-CG-4300         TCGA-CG-4301         TCGA-CG-4304 
"11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" 
        TCGA-CG-4305         TCGA-CG-4306         TCGA-CG-4436 
"11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" 
        TCGA-CG-4437         TCGA-CG-4438         TCGA-CG-4440 
"11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" 
        TCGA-CG-4441         TCGA-CG-4443         TCGA-CG-4444 
"11P LOSS WILD-TYPE"       "11P LOSS CNV" "11P LOSS WILD-TYPE" 
        TCGA-CG-4449         TCGA-CG-4455         TCGA-CG-4460 
"11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE"       "11P LOSS CNV" 
        TCGA-CG-4462         TCGA-CG-4465         TCGA-CG-4466 
"11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" 
        TCGA-CG-4469         TCGA-CG-4472         TCGA-CG-4474 
"11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" 
        TCGA-CG-4477         TCGA-CG-5716         TCGA-CG-5717 
      "11P LOSS CNV" "11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" 
        TCGA-CG-5718         TCGA-CG-5719         TCGA-CG-5720 
"11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" 
        TCGA-CG-5721         TCGA-CG-5722         TCGA-CG-5723 
"11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" 
        TCGA-CG-5724         TCGA-CG-5725         TCGA-CG-5726 
      "11P LOSS CNV" "11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" 
        TCGA-CG-5727         TCGA-CG-5728         TCGA-CG-5730 
"11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE"       "11P LOSS CNV" 
        TCGA-CG-5732         TCGA-CG-5733         TCGA-CG-5734 
"11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" 
        TCGA-D7-5577         TCGA-D7-5578         TCGA-D7-5579 
"11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" 
        TCGA-D7-6518         TCGA-D7-6519         TCGA-D7-6520 
"11P LOSS WILD-TYPE"       "11P LOSS CNV" "11P LOSS WILD-TYPE" 
        TCGA-D7-6521         TCGA-D7-6522         TCGA-D7-6524 
"11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" 
        TCGA-D7-6525         TCGA-D7-6526         TCGA-D7-6527 
"11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" 
        TCGA-D7-6528         TCGA-D7-6815         TCGA-D7-6817 
"11P LOSS WILD-TYPE"       "11P LOSS CNV" "11P LOSS WILD-TYPE" 
        TCGA-D7-6818         TCGA-D7-6820         TCGA-D7-6822 
"11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" 
        TCGA-EQ-5647         TCGA-EQ-8122         TCGA-F1-6177 
"11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" 
        TCGA-F1-6874         TCGA-F1-6875         TCGA-FP-7735 
"11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" 
        TCGA-FP-7829         TCGA-FP-7916         TCGA-FP-7998 
"11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" 
        TCGA-FP-8099         TCGA-FP-8209         TCGA-FP-8210 
"11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" 
        TCGA-FP-8631         TCGA-HJ-7597         TCGA-IN-7806 
"11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" 
        TCGA-IN-7808         TCGA-IP-7968 
"11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" 
        TCGA-B7-5816         TCGA-B7-5818         TCGA-BR-6452 
"11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" 
        TCGA-BR-6455         TCGA-BR-6457         TCGA-BR-6458 
"11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" 
        TCGA-BR-6563         TCGA-BR-6564         TCGA-BR-6565 
"11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" 
        TCGA-BR-6566         TCGA-BR-6705         TCGA-BR-6706 
"11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" 
        TCGA-BR-6707         TCGA-BR-6709         TCGA-BR-6710 
"11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" 
        TCGA-BR-6801         TCGA-BR-6802         TCGA-BR-6803 
"11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" 
        TCGA-BR-6852         TCGA-BR-7196         TCGA-BR-7197 
"11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" 
        TCGA-BR-7703         TCGA-BR-7704         TCGA-BR-7707 
"11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" 
        TCGA-BR-7715         TCGA-BR-7716         TCGA-BR-7717 
"11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" 
        TCGA-BR-7722         TCGA-BR-7723         TCGA-BR-7851 
"11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" 
        TCGA-BR-7901         TCGA-BR-7957         TCGA-BR-7958 
"11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" 
        TCGA-BR-7959         TCGA-BR-8059         TCGA-BR-8060 
"11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" 
        TCGA-BR-8077         TCGA-BR-8078         TCGA-BR-8080 
"11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" 
        TCGA-BR-8081         TCGA-BR-8284         TCGA-BR-8285 
"11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" 
        TCGA-BR-8286         TCGA-BR-8289         TCGA-BR-8291 
"11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" 
        TCGA-BR-8295         TCGA-BR-8296         TCGA-BR-8297 
"11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" 
        TCGA-BR-8592         TCGA-BR-A4IU         TCGA-BR-A4IV 
"11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" 
        TCGA-BR-A4IY         TCGA-BR-A4IZ         TCGA-BR-A4J1 
"11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE"       "11P LOSS CNV" 
        TCGA-BR-A4J2         TCGA-BR-A4J4         TCGA-BR-A4J5 
"11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" 
        TCGA-BR-A4J6         TCGA-BR-A4J8         TCGA-BR-A4J9 
"11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" 
        TCGA-BR-A4PF         TCGA-BR-A4QI         TCGA-BR-A4QL 
"11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" 
        TCGA-CD-5798         TCGA-CD-5799         TCGA-CD-5800 
"11P LOSS WILD-TYPE"       "11P LOSS CNV" "11P LOSS WILD-TYPE" 
        TCGA-CD-5801         TCGA-CD-5802         TCGA-CD-5803 
"11P LOSS WILD-TYPE"       "11P LOSS CNV" "11P LOSS WILD-TYPE" 
        TCGA-CG-4300         TCGA-CG-4301         TCGA-CG-4304 
"11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" 
        TCGA-CG-4305         TCGA-CG-4306         TCGA-CG-4436 
"11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" 
        TCGA-CG-4437         TCGA-CG-4438         TCGA-CG-4440 
"11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" 
        TCGA-CG-4441         TCGA-CG-4443         TCGA-CG-4444 
"11P LOSS WILD-TYPE"       "11P LOSS CNV" "11P LOSS WILD-TYPE" 
        TCGA-CG-4449         TCGA-CG-4455         TCGA-CG-4460 
"11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE"       "11P LOSS CNV" 
        TCGA-CG-4462         TCGA-CG-4465         TCGA-CG-4466 
"11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" 
        TCGA-CG-4469         TCGA-CG-4472         TCGA-CG-4474 
"11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" 
        TCGA-CG-4477         TCGA-CG-5716         TCGA-CG-5717 
      "11P LOSS CNV" "11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" 
        TCGA-CG-5718         TCGA-CG-5719         TCGA-CG-5720 
"11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" 
        TCGA-CG-5721         TCGA-CG-5722         TCGA-CG-5723 
"11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" 
        TCGA-CG-5724         TCGA-CG-5725         TCGA-CG-5726 
      "11P LOSS CNV" "11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" 
        TCGA-CG-5727         TCGA-CG-5728         TCGA-CG-5730 
"11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE"       "11P LOSS CNV" 
        TCGA-CG-5732         TCGA-CG-5733         TCGA-CG-5734 
"11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" 
        TCGA-D7-5577         TCGA-D7-5578         TCGA-D7-5579 
"11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" 
        TCGA-D7-6518         TCGA-D7-6519         TCGA-D7-6520 
"11P LOSS WILD-TYPE"       "11P LOSS CNV" "11P LOSS WILD-TYPE" 
        TCGA-D7-6521         TCGA-D7-6522         TCGA-D7-6524 
"11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" 
        TCGA-D7-6525         TCGA-D7-6526         TCGA-D7-6527 
"11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" 
        TCGA-D7-6528         TCGA-D7-6815         TCGA-D7-6817 
"11P LOSS WILD-TYPE"       "11P LOSS CNV" "11P LOSS WILD-TYPE" 
        TCGA-D7-6818         TCGA-D7-6820         TCGA-D7-6822 
"11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" 
        TCGA-EQ-5647         TCGA-EQ-8122         TCGA-F1-6177 
"11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" 
        TCGA-F1-6874         TCGA-F1-6875         TCGA-FP-7735 
"11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" 
        TCGA-FP-7829         TCGA-FP-7916         TCGA-FP-7998 
"11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" 
        TCGA-FP-8099         TCGA-FP-8209         TCGA-FP-8210 
"11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" 
        TCGA-FP-8631         TCGA-HJ-7597         TCGA-IN-7806 
"11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" 
        TCGA-IN-7808         TCGA-IP-7968 
"11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" 
[1] "hr=" "1.7"
D56V2, continuous
D56V3, binary
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  11P LOSS CNV          5    7
  11P LOSS WILD-TYPE   67  101
        clus
vv       11P LOSS CNV 11P LOSS WILD-TYPE
  FEMALE            5                 67
  MALE              7                101
                    vv
clus                 STOMACH  ADENOCARCINOMA  DIFFUSE TYPE
  11P LOSS CNV                                           0
  11P LOSS WILD-TYPE                                    10
                    vv
clus                 STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  11P LOSS CNV                                                            1
  11P LOSS WILD-TYPE                                                     15
                    vv
clus                 STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  11P LOSS CNV                                                                       0
  11P LOSS WILD-TYPE                                                                 8
                    vv
clus                 STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE
  11P LOSS CNV                                                              0
  11P LOSS WILD-TYPE                                                        3
                    vv
clus                 STOMACH ADENOCARCINOMA  SIGNET RING TYPE
  11P LOSS CNV                                              0
  11P LOSS WILD-TYPE                                        1
                    vv
clus                 STOMACH ADENOCARCINOMA - DIFFUSE TYPE
  11P LOSS CNV                                           2
  11P LOSS WILD-TYPE                                    14
                    vv
clus                 STOMACH ADENOCARCINOMA - NOT OTHERWISE SPECIFIED (NOS)
  11P LOSS CNV                                                            2
  11P LOSS WILD-TYPE                                                     71
                    vv
clus                 STOMACH INTESTINAL ADENOCARCINOMA - MUCINOUS TYPE
  11P LOSS CNV                                                       0
  11P LOSS WILD-TYPE                                                 7
                    vv
clus                 STOMACH INTESTINAL ADENOCARCINOMA - PAPILLARY TYPE
  11P LOSS CNV                                                        0
  11P LOSS WILD-TYPE                                                  3
                    vv
clus                 STOMACH INTESTINAL ADENOCARCINOMA - TUBULAR TYPE
  11P LOSS CNV                                                      2
  11P LOSS WILD-TYPE                                                8
                    vv
clus                 STOMACH INTESTINAL ADENOCARCINOMA - TYPE NOT OTHERWISE SPECIFIED (NOS)
  11P LOSS CNV                                                                            5
  11P LOSS WILD-TYPE                                                                     23
D56V4, multiclass
                    vv
clus                 T1 T2 T3 T4
  11P LOSS CNV        1  7  2  1
  11P LOSS WILD-TYPE  5 45 54 17
D56V5, multiclass
    clus
vv   11P LOSS CNV 11P LOSS WILD-TYPE
  T1            1                  5
  T2            7                 45
  T3            2                 54
  T4            1                 17
                    vv
clus                 N0 N1 N2 N3
  11P LOSS CNV        3  5  1  1
  11P LOSS WILD-TYPE 41 44 22 14
D56V6, multiclass
    clus
vv   11P LOSS CNV 11P LOSS WILD-TYPE
  N0            3                 41
  N1            5                 44
  N2            1                 22
  N3            1                 14
                    vv
clus                  M0  M1  MX
  11P LOSS CNV         8   3   0
  11P LOSS WILD-TYPE 110  13   8
D56V7, multiclass
    clus
vv   11P LOSS CNV 11P LOSS WILD-TYPE
  M0            8                110
  M1            3                 13
  MX            0                  8
                    vv
clus                  I II III IV
  11P LOSS CNV        2  3   2  3
  11P LOSS WILD-TYPE 22 34  37 23
D56V8, multiclass
     clus
vv    11P LOSS CNV 11P LOSS WILD-TYPE
  I              2                 22
  II             3                 34
  III            2                 37
  IV             3                 23
D56V9, binary
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  11P LOSS CNV          0   12
  11P LOSS WILD-TYPE    5  163
     clus
vv    11P LOSS CNV 11P LOSS WILD-TYPE
  NO             0                  5
  YES           12                163
                    vv
clus                  R0  R1  R2  RX
  11P LOSS CNV         5   0   3   2
  11P LOSS WILD-TYPE 120   7   9  23
D56V10, multiclass
    clus
vv   11P LOSS CNV 11P LOSS WILD-TYPE
  R0            5                120
  R1            0                  7
  R2            3                  9
  RX            2                 23
D56V11, continuous

Clustering(57) Variable = 11q loss
D57V1, survival
                    sevent
clus2                  0   1
  11Q LOSS CNV         6   3
  11Q LOSS WILD-TYPE 118  16
      11Q LOSS CNV 11Q LOSS WILD-TYPE 
                 9                134 
      11Q LOSS CNV 11Q LOSS WILD-TYPE 
                 3                 16 
$`11Q LOSS CNV`
TCGA-BR-A4J1 TCGA-BR-A4PF TCGA-CD-5799 TCGA-CD-5802 TCGA-CG-4437 TCGA-CG-4443 
        0.72         0.72         0.69         0.30         8.05        29.98 
TCGA-CG-5724 TCGA-D7-6815 TCGA-EQ-5647 
       12.03         3.65         0.62 

$`11Q LOSS WILD-TYPE`
TCGA-B7-5816 TCGA-B7-5818 TCGA-BR-6452 TCGA-BR-6455 TCGA-BR-6457 TCGA-BR-6458 
        5.62         0.10         0.95         1.41         1.35         1.35 
TCGA-BR-6563 TCGA-BR-6564 TCGA-BR-6565 TCGA-BR-6566 TCGA-BR-6705 TCGA-BR-6706 
        0.85         0.82         0.62         0.62         1.71         2.17 
TCGA-BR-6707 TCGA-BR-6709 TCGA-BR-6710 TCGA-BR-6801 TCGA-BR-6802 TCGA-BR-6803 
        0.99         1.22         0.66         1.12         0.76         0.66 
TCGA-BR-6852 TCGA-BR-7196 TCGA-BR-7197 TCGA-BR-7703 TCGA-BR-7704 TCGA-BR-7707 
        0.26         1.22         1.48         0.46         1.25         0.13 
TCGA-BR-7715 TCGA-BR-7716 TCGA-BR-7717 TCGA-BR-7722 TCGA-BR-7723 TCGA-BR-7851 
        1.05         0.82         0.69         0.16         4.54         0.99 
TCGA-BR-7901 TCGA-BR-7957 TCGA-BR-7958 TCGA-BR-7959 TCGA-BR-8059 TCGA-BR-8060 
        0.95         0.69         0.16         1.08         0.82         1.32 
TCGA-BR-8077 TCGA-BR-8078 TCGA-BR-8080 TCGA-BR-8081 TCGA-BR-8284 TCGA-BR-8285 
        0.69         0.95         0.49         0.46         0.72         0.26 
TCGA-BR-8286 TCGA-BR-8289 TCGA-BR-8291 TCGA-BR-8295 TCGA-BR-8296 TCGA-BR-8297 
        0.43         0.26         1.18         1.55         1.48         0.76 
TCGA-BR-8592 TCGA-BR-A4IU TCGA-BR-A4IV TCGA-BR-A4IY TCGA-BR-A4IZ TCGA-BR-A4J2 
        0.20         0.59         0.92         0.39         0.79         0.79 
TCGA-BR-A4J4 TCGA-BR-A4J5 TCGA-BR-A4J6 TCGA-BR-A4J8 TCGA-BR-A4J9 TCGA-BR-A4QI 
        0.53         0.43         0.13         0.23         0.10         0.49 
TCGA-BR-A4QL TCGA-CD-5798 TCGA-CD-5800 TCGA-CD-5801 TCGA-CD-5803 TCGA-CG-4300 
        2.24         0.82         0.36         0.49         0.07        20.02 
TCGA-CG-4301 TCGA-CG-4304 TCGA-CG-4305 TCGA-CG-4306 TCGA-CG-4436 TCGA-CG-4438 
        3.02        27.02        15.95         1.02        52.96        54.05 
TCGA-CG-4440 TCGA-CG-4441 TCGA-CG-4444 TCGA-CG-4449 TCGA-CG-4455 TCGA-CG-4460 
        4.01        14.01        47.05        19.07        12.03        21.99 
TCGA-CG-4462 TCGA-CG-4465 TCGA-CG-4466 TCGA-CG-4469 TCGA-CG-4472 TCGA-CG-4474 
        1.02         8.98        18.94         7.07        12.00         1.02 
TCGA-CG-4477 TCGA-CG-5716 TCGA-CG-5717 TCGA-CG-5718 TCGA-CG-5719 TCGA-CG-5720 
        1.02         1.02         6.94         1.02         1.02         0.99 
TCGA-CG-5721 TCGA-CG-5722 TCGA-CG-5723 TCGA-CG-5725 TCGA-CG-5726 TCGA-CG-5727 
        5.98         0.95        70.06        15.02        28.96        31.04 
TCGA-CG-5728 TCGA-CG-5730 TCGA-CG-5732 TCGA-CG-5733 TCGA-CG-5734 TCGA-D7-5577 
       65.10         4.01        55.04        21.07         7.99         8.65 
TCGA-D7-5578 TCGA-D7-5579 TCGA-D7-6518 TCGA-D7-6519 TCGA-D7-6520 TCGA-D7-6521 
        3.58         4.54         9.80        15.65         9.63         8.19 
TCGA-D7-6522 TCGA-D7-6524 TCGA-D7-6525 TCGA-D7-6526 TCGA-D7-6527 TCGA-D7-6528 
        6.90         0.69         5.95         6.61         4.14         1.68 
TCGA-D7-6817 TCGA-D7-6818 TCGA-D7-6820 TCGA-D7-6822 TCGA-EQ-8122 TCGA-F1-6177 
        4.70         4.04         2.93         4.27         7.79         6.54 
TCGA-F1-6874 TCGA-F1-6875 TCGA-FP-7735 TCGA-FP-7829 TCGA-FP-7916 TCGA-FP-7998 
        2.01        72.23         0.39         0.20         3.02         3.58 
TCGA-FP-8099 TCGA-FP-8209 TCGA-FP-8210 TCGA-FP-8631 TCGA-HJ-7597 TCGA-IN-7806 
        1.02        59.05         5.03         0.56        26.43         6.87 
TCGA-IN-7808 TCGA-IP-7968 
        3.55         2.53 

      11Q LOSS CNV 11Q LOSS WILD-TYPE 
              0.30               0.07 
      11Q LOSS CNV 11Q LOSS WILD-TYPE 
             29.98              72.23 
      11Q LOSS CNV 11Q LOSS WILD-TYPE 
             0.720              1.285 
[1] "0.3 - 30.0 (0.7)" "0.1 - 72.2 (1.3)"
        TCGA-B7-5816         TCGA-B7-5818         TCGA-BR-6452 
"11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" 
        TCGA-BR-6455         TCGA-BR-6457         TCGA-BR-6458 
"11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" 
        TCGA-BR-6563         TCGA-BR-6564         TCGA-BR-6565 
"11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" 
        TCGA-BR-6566         TCGA-BR-6705         TCGA-BR-6706 
"11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" 
        TCGA-BR-6707         TCGA-BR-6709         TCGA-BR-6710 
"11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" 
        TCGA-BR-6801         TCGA-BR-6802         TCGA-BR-6803 
"11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" 
        TCGA-BR-6852         TCGA-BR-7196         TCGA-BR-7197 
"11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" 
        TCGA-BR-7703         TCGA-BR-7704         TCGA-BR-7707 
"11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" 
        TCGA-BR-7715         TCGA-BR-7716         TCGA-BR-7717 
"11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" 
        TCGA-BR-7722         TCGA-BR-7723         TCGA-BR-7851 
"11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" 
        TCGA-BR-7901         TCGA-BR-7957         TCGA-BR-7958 
"11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" 
        TCGA-BR-7959         TCGA-BR-8059         TCGA-BR-8060 
"11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" 
        TCGA-BR-8077         TCGA-BR-8078         TCGA-BR-8080 
"11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" 
        TCGA-BR-8081         TCGA-BR-8284         TCGA-BR-8285 
"11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" 
        TCGA-BR-8286         TCGA-BR-8289         TCGA-BR-8291 
"11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" 
        TCGA-BR-8295         TCGA-BR-8296         TCGA-BR-8297 
"11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" 
        TCGA-BR-8592         TCGA-BR-A4IU         TCGA-BR-A4IV 
"11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" 
        TCGA-BR-A4IY         TCGA-BR-A4IZ         TCGA-BR-A4J1 
"11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE"       "11Q LOSS CNV" 
        TCGA-BR-A4J2         TCGA-BR-A4J4         TCGA-BR-A4J5 
"11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" 
        TCGA-BR-A4J6         TCGA-BR-A4J8         TCGA-BR-A4J9 
"11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" 
        TCGA-BR-A4PF         TCGA-BR-A4QI         TCGA-BR-A4QL 
      "11Q LOSS CNV" "11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" 
        TCGA-CD-5798         TCGA-CD-5799         TCGA-CD-5800 
"11Q LOSS WILD-TYPE"       "11Q LOSS CNV" "11Q LOSS WILD-TYPE" 
        TCGA-CD-5801         TCGA-CD-5802         TCGA-CD-5803 
"11Q LOSS WILD-TYPE"       "11Q LOSS CNV" "11Q LOSS WILD-TYPE" 
        TCGA-CG-4300         TCGA-CG-4301         TCGA-CG-4304 
"11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" 
        TCGA-CG-4305         TCGA-CG-4306         TCGA-CG-4436 
"11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" 
        TCGA-CG-4437         TCGA-CG-4438         TCGA-CG-4440 
      "11Q LOSS CNV" "11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" 
        TCGA-CG-4441         TCGA-CG-4443         TCGA-CG-4444 
"11Q LOSS WILD-TYPE"       "11Q LOSS CNV" "11Q LOSS WILD-TYPE" 
        TCGA-CG-4449         TCGA-CG-4455         TCGA-CG-4460 
"11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" 
        TCGA-CG-4462         TCGA-CG-4465         TCGA-CG-4466 
"11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" 
        TCGA-CG-4469         TCGA-CG-4472         TCGA-CG-4474 
"11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" 
        TCGA-CG-4477         TCGA-CG-5716         TCGA-CG-5717 
"11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" 
        TCGA-CG-5718         TCGA-CG-5719         TCGA-CG-5720 
"11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" 
        TCGA-CG-5721         TCGA-CG-5722         TCGA-CG-5723 
"11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" 
        TCGA-CG-5724         TCGA-CG-5725         TCGA-CG-5726 
      "11Q LOSS CNV" "11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" 
        TCGA-CG-5727         TCGA-CG-5728         TCGA-CG-5730 
"11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" 
        TCGA-CG-5732         TCGA-CG-5733         TCGA-CG-5734 
"11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" 
        TCGA-D7-5577         TCGA-D7-5578         TCGA-D7-5579 
"11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" 
        TCGA-D7-6518         TCGA-D7-6519         TCGA-D7-6520 
"11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" 
        TCGA-D7-6521         TCGA-D7-6522         TCGA-D7-6524 
"11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" 
        TCGA-D7-6525         TCGA-D7-6526         TCGA-D7-6527 
"11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" 
        TCGA-D7-6528         TCGA-D7-6815         TCGA-D7-6817 
"11Q LOSS WILD-TYPE"       "11Q LOSS CNV" "11Q LOSS WILD-TYPE" 
        TCGA-D7-6818         TCGA-D7-6820         TCGA-D7-6822 
"11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" 
        TCGA-EQ-5647         TCGA-EQ-8122         TCGA-F1-6177 
      "11Q LOSS CNV" "11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" 
        TCGA-F1-6874         TCGA-F1-6875         TCGA-FP-7735 
"11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" 
        TCGA-FP-7829         TCGA-FP-7916         TCGA-FP-7998 
"11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" 
        TCGA-FP-8099         TCGA-FP-8209         TCGA-FP-8210 
"11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" 
        TCGA-FP-8631         TCGA-HJ-7597         TCGA-IN-7806 
"11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" 
        TCGA-IN-7808         TCGA-IP-7968 
"11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" 
        TCGA-B7-5816         TCGA-B7-5818         TCGA-BR-6452 
"11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" 
        TCGA-BR-6455         TCGA-BR-6457         TCGA-BR-6458 
"11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" 
        TCGA-BR-6563         TCGA-BR-6564         TCGA-BR-6565 
"11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" 
        TCGA-BR-6566         TCGA-BR-6705         TCGA-BR-6706 
"11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" 
        TCGA-BR-6707         TCGA-BR-6709         TCGA-BR-6710 
"11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" 
        TCGA-BR-6801         TCGA-BR-6802         TCGA-BR-6803 
"11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" 
        TCGA-BR-6852         TCGA-BR-7196         TCGA-BR-7197 
"11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" 
        TCGA-BR-7703         TCGA-BR-7704         TCGA-BR-7707 
"11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" 
        TCGA-BR-7715         TCGA-BR-7716         TCGA-BR-7717 
"11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" 
        TCGA-BR-7722         TCGA-BR-7723         TCGA-BR-7851 
"11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" 
        TCGA-BR-7901         TCGA-BR-7957         TCGA-BR-7958 
"11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" 
        TCGA-BR-7959         TCGA-BR-8059         TCGA-BR-8060 
"11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" 
        TCGA-BR-8077         TCGA-BR-8078         TCGA-BR-8080 
"11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" 
        TCGA-BR-8081         TCGA-BR-8284         TCGA-BR-8285 
"11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" 
        TCGA-BR-8286         TCGA-BR-8289         TCGA-BR-8291 
"11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" 
        TCGA-BR-8295         TCGA-BR-8296         TCGA-BR-8297 
"11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" 
        TCGA-BR-8592         TCGA-BR-A4IU         TCGA-BR-A4IV 
"11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" 
        TCGA-BR-A4IY         TCGA-BR-A4IZ         TCGA-BR-A4J1 
"11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE"       "11Q LOSS CNV" 
        TCGA-BR-A4J2         TCGA-BR-A4J4         TCGA-BR-A4J5 
"11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" 
        TCGA-BR-A4J6         TCGA-BR-A4J8         TCGA-BR-A4J9 
"11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" 
        TCGA-BR-A4PF         TCGA-BR-A4QI         TCGA-BR-A4QL 
      "11Q LOSS CNV" "11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" 
        TCGA-CD-5798         TCGA-CD-5799         TCGA-CD-5800 
"11Q LOSS WILD-TYPE"       "11Q LOSS CNV" "11Q LOSS WILD-TYPE" 
        TCGA-CD-5801         TCGA-CD-5802         TCGA-CD-5803 
"11Q LOSS WILD-TYPE"       "11Q LOSS CNV" "11Q LOSS WILD-TYPE" 
        TCGA-CG-4300         TCGA-CG-4301         TCGA-CG-4304 
"11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" 
        TCGA-CG-4305         TCGA-CG-4306         TCGA-CG-4436 
"11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" 
        TCGA-CG-4437         TCGA-CG-4438         TCGA-CG-4440 
      "11Q LOSS CNV" "11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" 
        TCGA-CG-4441         TCGA-CG-4443         TCGA-CG-4444 
"11Q LOSS WILD-TYPE"       "11Q LOSS CNV" "11Q LOSS WILD-TYPE" 
        TCGA-CG-4449         TCGA-CG-4455         TCGA-CG-4460 
"11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" 
        TCGA-CG-4462         TCGA-CG-4465         TCGA-CG-4466 
"11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" 
        TCGA-CG-4469         TCGA-CG-4472         TCGA-CG-4474 
"11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" 
        TCGA-CG-4477         TCGA-CG-5716         TCGA-CG-5717 
"11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" 
        TCGA-CG-5718         TCGA-CG-5719         TCGA-CG-5720 
"11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" 
        TCGA-CG-5721         TCGA-CG-5722         TCGA-CG-5723 
"11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" 
        TCGA-CG-5724         TCGA-CG-5725         TCGA-CG-5726 
      "11Q LOSS CNV" "11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" 
        TCGA-CG-5727         TCGA-CG-5728         TCGA-CG-5730 
"11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" 
        TCGA-CG-5732         TCGA-CG-5733         TCGA-CG-5734 
"11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" 
        TCGA-D7-5577         TCGA-D7-5578         TCGA-D7-5579 
"11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" 
        TCGA-D7-6518         TCGA-D7-6519         TCGA-D7-6520 
"11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" 
        TCGA-D7-6521         TCGA-D7-6522         TCGA-D7-6524 
"11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" 
        TCGA-D7-6525         TCGA-D7-6526         TCGA-D7-6527 
"11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" 
        TCGA-D7-6528         TCGA-D7-6815         TCGA-D7-6817 
"11Q LOSS WILD-TYPE"       "11Q LOSS CNV" "11Q LOSS WILD-TYPE" 
        TCGA-D7-6818         TCGA-D7-6820         TCGA-D7-6822 
"11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" 
        TCGA-EQ-5647         TCGA-EQ-8122         TCGA-F1-6177 
      "11Q LOSS CNV" "11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" 
        TCGA-F1-6874         TCGA-F1-6875         TCGA-FP-7735 
"11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" 
        TCGA-FP-7829         TCGA-FP-7916         TCGA-FP-7998 
"11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" 
        TCGA-FP-8099         TCGA-FP-8209         TCGA-FP-8210 
"11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" 
        TCGA-FP-8631         TCGA-HJ-7597         TCGA-IN-7806 
"11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" 
        TCGA-IN-7808         TCGA-IP-7968 
"11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" 
        TCGA-B7-5816         TCGA-B7-5818         TCGA-BR-6452 
"11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" 
        TCGA-BR-6455         TCGA-BR-6457         TCGA-BR-6458 
"11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" 
        TCGA-BR-6563         TCGA-BR-6564         TCGA-BR-6565 
"11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" 
        TCGA-BR-6566         TCGA-BR-6705         TCGA-BR-6706 
"11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" 
        TCGA-BR-6707         TCGA-BR-6709         TCGA-BR-6710 
"11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" 
        TCGA-BR-6801         TCGA-BR-6802         TCGA-BR-6803 
"11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" 
        TCGA-BR-6852         TCGA-BR-7196         TCGA-BR-7197 
"11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" 
        TCGA-BR-7703         TCGA-BR-7704         TCGA-BR-7707 
"11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" 
        TCGA-BR-7715         TCGA-BR-7716         TCGA-BR-7717 
"11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" 
        TCGA-BR-7722         TCGA-BR-7723         TCGA-BR-7851 
"11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" 
        TCGA-BR-7901         TCGA-BR-7957         TCGA-BR-7958 
"11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" 
        TCGA-BR-7959         TCGA-BR-8059         TCGA-BR-8060 
"11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" 
        TCGA-BR-8077         TCGA-BR-8078         TCGA-BR-8080 
"11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" 
        TCGA-BR-8081         TCGA-BR-8284         TCGA-BR-8285 
"11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" 
        TCGA-BR-8286         TCGA-BR-8289         TCGA-BR-8291 
"11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" 
        TCGA-BR-8295         TCGA-BR-8296         TCGA-BR-8297 
"11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" 
        TCGA-BR-8592         TCGA-BR-A4IU         TCGA-BR-A4IV 
"11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" 
        TCGA-BR-A4IY         TCGA-BR-A4IZ         TCGA-BR-A4J1 
"11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE"       "11Q LOSS CNV" 
        TCGA-BR-A4J2         TCGA-BR-A4J4         TCGA-BR-A4J5 
"11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" 
        TCGA-BR-A4J6         TCGA-BR-A4J8         TCGA-BR-A4J9 
"11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" 
        TCGA-BR-A4PF         TCGA-BR-A4QI         TCGA-BR-A4QL 
      "11Q LOSS CNV" "11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" 
        TCGA-CD-5798         TCGA-CD-5799         TCGA-CD-5800 
"11Q LOSS WILD-TYPE"       "11Q LOSS CNV" "11Q LOSS WILD-TYPE" 
        TCGA-CD-5801         TCGA-CD-5802         TCGA-CD-5803 
"11Q LOSS WILD-TYPE"       "11Q LOSS CNV" "11Q LOSS WILD-TYPE" 
        TCGA-CG-4300         TCGA-CG-4301         TCGA-CG-4304 
"11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" 
        TCGA-CG-4305         TCGA-CG-4306         TCGA-CG-4436 
"11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" 
        TCGA-CG-4437         TCGA-CG-4438         TCGA-CG-4440 
      "11Q LOSS CNV" "11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" 
        TCGA-CG-4441         TCGA-CG-4443         TCGA-CG-4444 
"11Q LOSS WILD-TYPE"       "11Q LOSS CNV" "11Q LOSS WILD-TYPE" 
        TCGA-CG-4449         TCGA-CG-4455         TCGA-CG-4460 
"11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" 
        TCGA-CG-4462         TCGA-CG-4465         TCGA-CG-4466 
"11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" 
        TCGA-CG-4469         TCGA-CG-4472         TCGA-CG-4474 
"11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" 
        TCGA-CG-4477         TCGA-CG-5716         TCGA-CG-5717 
"11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" 
        TCGA-CG-5718         TCGA-CG-5719         TCGA-CG-5720 
"11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" 
        TCGA-CG-5721         TCGA-CG-5722         TCGA-CG-5723 
"11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" 
        TCGA-CG-5724         TCGA-CG-5725         TCGA-CG-5726 
      "11Q LOSS CNV" "11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" 
        TCGA-CG-5727         TCGA-CG-5728         TCGA-CG-5730 
"11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" 
        TCGA-CG-5732         TCGA-CG-5733         TCGA-CG-5734 
"11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" 
        TCGA-D7-5577         TCGA-D7-5578         TCGA-D7-5579 
"11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" 
        TCGA-D7-6518         TCGA-D7-6519         TCGA-D7-6520 
"11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" 
        TCGA-D7-6521         TCGA-D7-6522         TCGA-D7-6524 
"11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" 
        TCGA-D7-6525         TCGA-D7-6526         TCGA-D7-6527 
"11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" 
        TCGA-D7-6528         TCGA-D7-6815         TCGA-D7-6817 
"11Q LOSS WILD-TYPE"       "11Q LOSS CNV" "11Q LOSS WILD-TYPE" 
        TCGA-D7-6818         TCGA-D7-6820         TCGA-D7-6822 
"11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" 
        TCGA-EQ-5647         TCGA-EQ-8122         TCGA-F1-6177 
      "11Q LOSS CNV" "11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" 
        TCGA-F1-6874         TCGA-F1-6875         TCGA-FP-7735 
"11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" 
        TCGA-FP-7829         TCGA-FP-7916         TCGA-FP-7998 
"11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" 
        TCGA-FP-8099         TCGA-FP-8209         TCGA-FP-8210 
"11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" 
        TCGA-FP-8631         TCGA-HJ-7597         TCGA-IN-7806 
"11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" 
        TCGA-IN-7808         TCGA-IP-7968 
"11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" 
[1] "hr=" "2.9"
D57V2, continuous
D57V3, binary
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  11Q LOSS CNV          2    9
  11Q LOSS WILD-TYPE   70   99
        clus
vv       11Q LOSS CNV 11Q LOSS WILD-TYPE
  FEMALE            2                 70
  MALE              9                 99
                    vv
clus                 STOMACH  ADENOCARCINOMA  DIFFUSE TYPE
  11Q LOSS CNV                                           0
  11Q LOSS WILD-TYPE                                    10
                    vv
clus                 STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  11Q LOSS CNV                                                            2
  11Q LOSS WILD-TYPE                                                     14
                    vv
clus                 STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  11Q LOSS CNV                                                                       0
  11Q LOSS WILD-TYPE                                                                 8
                    vv
clus                 STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE
  11Q LOSS CNV                                                              0
  11Q LOSS WILD-TYPE                                                        3
                    vv
clus                 STOMACH ADENOCARCINOMA  SIGNET RING TYPE
  11Q LOSS CNV                                              0
  11Q LOSS WILD-TYPE                                        1
                    vv
clus                 STOMACH ADENOCARCINOMA - DIFFUSE TYPE
  11Q LOSS CNV                                           1
  11Q LOSS WILD-TYPE                                    15
                    vv
clus                 STOMACH ADENOCARCINOMA - NOT OTHERWISE SPECIFIED (NOS)
  11Q LOSS CNV                                                            3
  11Q LOSS WILD-TYPE                                                     70
                    vv
clus                 STOMACH INTESTINAL ADENOCARCINOMA - MUCINOUS TYPE
  11Q LOSS CNV                                                       0
  11Q LOSS WILD-TYPE                                                 7
                    vv
clus                 STOMACH INTESTINAL ADENOCARCINOMA - PAPILLARY TYPE
  11Q LOSS CNV                                                        0
  11Q LOSS WILD-TYPE                                                  3
                    vv
clus                 STOMACH INTESTINAL ADENOCARCINOMA - TUBULAR TYPE
  11Q LOSS CNV                                                      2
  11Q LOSS WILD-TYPE                                                8
                    vv
clus                 STOMACH INTESTINAL ADENOCARCINOMA - TYPE NOT OTHERWISE SPECIFIED (NOS)
  11Q LOSS CNV                                                                            3
  11Q LOSS WILD-TYPE                                                                     25
D57V4, multiclass
                    vv
clus                 T1 T2 T3 T4
  11Q LOSS CNV        1  5  2  1
  11Q LOSS WILD-TYPE  5 47 54 17
D57V5, multiclass
    clus
vv   11Q LOSS CNV 11Q LOSS WILD-TYPE
  T1            1                  5
  T2            5                 47
  T3            2                 54
  T4            1                 17
                    vv
clus                 N0 N1 N2 N3
  11Q LOSS CNV        2  3  1  2
  11Q LOSS WILD-TYPE 42 46 22 13
D57V6, multiclass
    clus
vv   11Q LOSS CNV 11Q LOSS WILD-TYPE
  N0            2                 42
  N1            3                 46
  N2            1                 22
  N3            2                 13
                    vv
clus                  M0  M1  MX
  11Q LOSS CNV         7   2   0
  11Q LOSS WILD-TYPE 111  14   8
D57V7, multiclass
    clus
vv   11Q LOSS CNV 11Q LOSS WILD-TYPE
  M0            7                111
  M1            2                 14
  MX            0                  8
                    vv
clus                  I II III IV
  11Q LOSS CNV        1  4   1  2
  11Q LOSS WILD-TYPE 23 33  38 24
D57V8, multiclass
     clus
vv    11Q LOSS CNV 11Q LOSS WILD-TYPE
  I              1                 23
  II             4                 33
  III            1                 38
  IV             2                 24
D57V9, binary
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  11Q LOSS CNV          0   11
  11Q LOSS WILD-TYPE    5  164
     clus
vv    11Q LOSS CNV 11Q LOSS WILD-TYPE
  NO             0                  5
  YES           11                164
                    vv
clus                  R0  R1  R2  RX
  11Q LOSS CNV         5   0   2   2
  11Q LOSS WILD-TYPE 120   7  10  23
D57V10, multiclass
    clus
vv   11Q LOSS CNV 11Q LOSS WILD-TYPE
  R0            5                120
  R1            0                  7
  R2            2                 10
  RX            2                 23
D57V11, continuous

Clustering(58) Variable = 12p loss
D58V1, survival
                    sevent
clus2                  0   1
  12P LOSS CNV        10   2
  12P LOSS WILD-TYPE 114  17
      12P LOSS CNV 12P LOSS WILD-TYPE 
                12                131 
      12P LOSS CNV 12P LOSS WILD-TYPE 
                 2                 17 
$`12P LOSS CNV`
TCGA-BR-7715 TCGA-BR-8060 TCGA-BR-A4J6 TCGA-CD-5800 TCGA-CD-5802 TCGA-CG-4436 
        1.05         1.32         0.13         0.36         0.30        52.96 
TCGA-CG-4443 TCGA-CG-4477 TCGA-CG-5725 TCGA-CG-5732 TCGA-D7-6822 TCGA-F1-6875 
       29.98         1.02        15.02        55.04         4.27        72.23 

$`12P LOSS WILD-TYPE`
TCGA-B7-5816 TCGA-B7-5818 TCGA-BR-6452 TCGA-BR-6455 TCGA-BR-6457 TCGA-BR-6458 
        5.62         0.10         0.95         1.41         1.35         1.35 
TCGA-BR-6563 TCGA-BR-6564 TCGA-BR-6565 TCGA-BR-6566 TCGA-BR-6705 TCGA-BR-6706 
        0.85         0.82         0.62         0.62         1.71         2.17 
TCGA-BR-6707 TCGA-BR-6709 TCGA-BR-6710 TCGA-BR-6801 TCGA-BR-6802 TCGA-BR-6803 
        0.99         1.22         0.66         1.12         0.76         0.66 
TCGA-BR-6852 TCGA-BR-7196 TCGA-BR-7197 TCGA-BR-7703 TCGA-BR-7704 TCGA-BR-7707 
        0.26         1.22         1.48         0.46         1.25         0.13 
TCGA-BR-7716 TCGA-BR-7717 TCGA-BR-7722 TCGA-BR-7723 TCGA-BR-7851 TCGA-BR-7901 
        0.82         0.69         0.16         4.54         0.99         0.95 
TCGA-BR-7957 TCGA-BR-7958 TCGA-BR-7959 TCGA-BR-8059 TCGA-BR-8077 TCGA-BR-8078 
        0.69         0.16         1.08         0.82         0.69         0.95 
TCGA-BR-8080 TCGA-BR-8081 TCGA-BR-8284 TCGA-BR-8285 TCGA-BR-8286 TCGA-BR-8289 
        0.49         0.46         0.72         0.26         0.43         0.26 
TCGA-BR-8291 TCGA-BR-8295 TCGA-BR-8296 TCGA-BR-8297 TCGA-BR-8592 TCGA-BR-A4IU 
        1.18         1.55         1.48         0.76         0.20         0.59 
TCGA-BR-A4IV TCGA-BR-A4IY TCGA-BR-A4IZ TCGA-BR-A4J1 TCGA-BR-A4J2 TCGA-BR-A4J4 
        0.92         0.39         0.79         0.72         0.79         0.53 
TCGA-BR-A4J5 TCGA-BR-A4J8 TCGA-BR-A4J9 TCGA-BR-A4PF TCGA-BR-A4QI TCGA-BR-A4QL 
        0.43         0.23         0.10         0.72         0.49         2.24 
TCGA-CD-5798 TCGA-CD-5799 TCGA-CD-5801 TCGA-CD-5803 TCGA-CG-4300 TCGA-CG-4301 
        0.82         0.69         0.49         0.07        20.02         3.02 
TCGA-CG-4304 TCGA-CG-4305 TCGA-CG-4306 TCGA-CG-4437 TCGA-CG-4438 TCGA-CG-4440 
       27.02        15.95         1.02         8.05        54.05         4.01 
TCGA-CG-4441 TCGA-CG-4444 TCGA-CG-4449 TCGA-CG-4455 TCGA-CG-4460 TCGA-CG-4462 
       14.01        47.05        19.07        12.03        21.99         1.02 
TCGA-CG-4465 TCGA-CG-4466 TCGA-CG-4469 TCGA-CG-4472 TCGA-CG-4474 TCGA-CG-5716 
        8.98        18.94         7.07        12.00         1.02         1.02 
TCGA-CG-5717 TCGA-CG-5718 TCGA-CG-5719 TCGA-CG-5720 TCGA-CG-5721 TCGA-CG-5722 
        6.94         1.02         1.02         0.99         5.98         0.95 
TCGA-CG-5723 TCGA-CG-5724 TCGA-CG-5726 TCGA-CG-5727 TCGA-CG-5728 TCGA-CG-5730 
       70.06        12.03        28.96        31.04        65.10         4.01 
TCGA-CG-5733 TCGA-CG-5734 TCGA-D7-5577 TCGA-D7-5578 TCGA-D7-5579 TCGA-D7-6518 
       21.07         7.99         8.65         3.58         4.54         9.80 
TCGA-D7-6519 TCGA-D7-6520 TCGA-D7-6521 TCGA-D7-6522 TCGA-D7-6524 TCGA-D7-6525 
       15.65         9.63         8.19         6.90         0.69         5.95 
TCGA-D7-6526 TCGA-D7-6527 TCGA-D7-6528 TCGA-D7-6815 TCGA-D7-6817 TCGA-D7-6818 
        6.61         4.14         1.68         3.65         4.70         4.04 
TCGA-D7-6820 TCGA-EQ-5647 TCGA-EQ-8122 TCGA-F1-6177 TCGA-F1-6874 TCGA-FP-7735 
        2.93         0.62         7.79         6.54         2.01         0.39 
TCGA-FP-7829 TCGA-FP-7916 TCGA-FP-7998 TCGA-FP-8099 TCGA-FP-8209 TCGA-FP-8210 
        0.20         3.02         3.58         1.02        59.05         5.03 
TCGA-FP-8631 TCGA-HJ-7597 TCGA-IN-7806 TCGA-IN-7808 TCGA-IP-7968 
        0.56        26.43         6.87         3.55         2.53 

      12P LOSS CNV 12P LOSS WILD-TYPE 
              0.13               0.07 
      12P LOSS CNV 12P LOSS WILD-TYPE 
             72.23              70.06 
      12P LOSS CNV 12P LOSS WILD-TYPE 
             2.795              1.220 
[1] "0.1 - 72.2 (2.8)" "0.1 - 70.1 (1.2)"
        TCGA-B7-5816         TCGA-B7-5818         TCGA-BR-6452 
"12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" 
        TCGA-BR-6455         TCGA-BR-6457         TCGA-BR-6458 
"12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" 
        TCGA-BR-6563         TCGA-BR-6564         TCGA-BR-6565 
"12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" 
        TCGA-BR-6566         TCGA-BR-6705         TCGA-BR-6706 
"12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" 
        TCGA-BR-6707         TCGA-BR-6709         TCGA-BR-6710 
"12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" 
        TCGA-BR-6801         TCGA-BR-6802         TCGA-BR-6803 
"12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" 
        TCGA-BR-6852         TCGA-BR-7196         TCGA-BR-7197 
"12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" 
        TCGA-BR-7703         TCGA-BR-7704         TCGA-BR-7707 
"12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" 
        TCGA-BR-7715         TCGA-BR-7716         TCGA-BR-7717 
      "12P LOSS CNV" "12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" 
        TCGA-BR-7722         TCGA-BR-7723         TCGA-BR-7851 
"12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" 
        TCGA-BR-7901         TCGA-BR-7957         TCGA-BR-7958 
"12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" 
        TCGA-BR-7959         TCGA-BR-8059         TCGA-BR-8060 
"12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE"       "12P LOSS CNV" 
        TCGA-BR-8077         TCGA-BR-8078         TCGA-BR-8080 
"12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" 
        TCGA-BR-8081         TCGA-BR-8284         TCGA-BR-8285 
"12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" 
        TCGA-BR-8286         TCGA-BR-8289         TCGA-BR-8291 
"12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" 
        TCGA-BR-8295         TCGA-BR-8296         TCGA-BR-8297 
"12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" 
        TCGA-BR-8592         TCGA-BR-A4IU         TCGA-BR-A4IV 
"12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" 
        TCGA-BR-A4IY         TCGA-BR-A4IZ         TCGA-BR-A4J1 
"12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" 
        TCGA-BR-A4J2         TCGA-BR-A4J4         TCGA-BR-A4J5 
"12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" 
        TCGA-BR-A4J6         TCGA-BR-A4J8         TCGA-BR-A4J9 
      "12P LOSS CNV" "12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" 
        TCGA-BR-A4PF         TCGA-BR-A4QI         TCGA-BR-A4QL 
"12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" 
        TCGA-CD-5798         TCGA-CD-5799         TCGA-CD-5800 
"12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE"       "12P LOSS CNV" 
        TCGA-CD-5801         TCGA-CD-5802         TCGA-CD-5803 
"12P LOSS WILD-TYPE"       "12P LOSS CNV" "12P LOSS WILD-TYPE" 
        TCGA-CG-4300         TCGA-CG-4301         TCGA-CG-4304 
"12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" 
        TCGA-CG-4305         TCGA-CG-4306         TCGA-CG-4436 
"12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE"       "12P LOSS CNV" 
        TCGA-CG-4437         TCGA-CG-4438         TCGA-CG-4440 
"12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" 
        TCGA-CG-4441         TCGA-CG-4443         TCGA-CG-4444 
"12P LOSS WILD-TYPE"       "12P LOSS CNV" "12P LOSS WILD-TYPE" 
        TCGA-CG-4449         TCGA-CG-4455         TCGA-CG-4460 
"12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" 
        TCGA-CG-4462         TCGA-CG-4465         TCGA-CG-4466 
"12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" 
        TCGA-CG-4469         TCGA-CG-4472         TCGA-CG-4474 
"12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" 
        TCGA-CG-4477         TCGA-CG-5716         TCGA-CG-5717 
      "12P LOSS CNV" "12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" 
        TCGA-CG-5718         TCGA-CG-5719         TCGA-CG-5720 
"12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" 
        TCGA-CG-5721         TCGA-CG-5722         TCGA-CG-5723 
"12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" 
        TCGA-CG-5724         TCGA-CG-5725         TCGA-CG-5726 
"12P LOSS WILD-TYPE"       "12P LOSS CNV" "12P LOSS WILD-TYPE" 
        TCGA-CG-5727         TCGA-CG-5728         TCGA-CG-5730 
"12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" 
        TCGA-CG-5732         TCGA-CG-5733         TCGA-CG-5734 
      "12P LOSS CNV" "12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" 
        TCGA-D7-5577         TCGA-D7-5578         TCGA-D7-5579 
"12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" 
        TCGA-D7-6518         TCGA-D7-6519         TCGA-D7-6520 
"12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" 
        TCGA-D7-6521         TCGA-D7-6522         TCGA-D7-6524 
"12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" 
        TCGA-D7-6525         TCGA-D7-6526         TCGA-D7-6527 
"12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" 
        TCGA-D7-6528         TCGA-D7-6815         TCGA-D7-6817 
"12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" 
        TCGA-D7-6818         TCGA-D7-6820         TCGA-D7-6822 
"12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE"       "12P LOSS CNV" 
        TCGA-EQ-5647         TCGA-EQ-8122         TCGA-F1-6177 
"12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" 
        TCGA-F1-6874         TCGA-F1-6875         TCGA-FP-7735 
"12P LOSS WILD-TYPE"       "12P LOSS CNV" "12P LOSS WILD-TYPE" 
        TCGA-FP-7829         TCGA-FP-7916         TCGA-FP-7998 
"12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" 
        TCGA-FP-8099         TCGA-FP-8209         TCGA-FP-8210 
"12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" 
        TCGA-FP-8631         TCGA-HJ-7597         TCGA-IN-7806 
"12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" 
        TCGA-IN-7808         TCGA-IP-7968 
"12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" 
        TCGA-B7-5816         TCGA-B7-5818         TCGA-BR-6452 
"12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" 
        TCGA-BR-6455         TCGA-BR-6457         TCGA-BR-6458 
"12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" 
        TCGA-BR-6563         TCGA-BR-6564         TCGA-BR-6565 
"12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" 
        TCGA-BR-6566         TCGA-BR-6705         TCGA-BR-6706 
"12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" 
        TCGA-BR-6707         TCGA-BR-6709         TCGA-BR-6710 
"12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" 
        TCGA-BR-6801         TCGA-BR-6802         TCGA-BR-6803 
"12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" 
        TCGA-BR-6852         TCGA-BR-7196         TCGA-BR-7197 
"12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" 
        TCGA-BR-7703         TCGA-BR-7704         TCGA-BR-7707 
"12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" 
        TCGA-BR-7715         TCGA-BR-7716         TCGA-BR-7717 
      "12P LOSS CNV" "12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" 
        TCGA-BR-7722         TCGA-BR-7723         TCGA-BR-7851 
"12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" 
        TCGA-BR-7901         TCGA-BR-7957         TCGA-BR-7958 
"12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" 
        TCGA-BR-7959         TCGA-BR-8059         TCGA-BR-8060 
"12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE"       "12P LOSS CNV" 
        TCGA-BR-8077         TCGA-BR-8078         TCGA-BR-8080 
"12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" 
        TCGA-BR-8081         TCGA-BR-8284         TCGA-BR-8285 
"12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" 
        TCGA-BR-8286         TCGA-BR-8289         TCGA-BR-8291 
"12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" 
        TCGA-BR-8295         TCGA-BR-8296         TCGA-BR-8297 
"12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" 
        TCGA-BR-8592         TCGA-BR-A4IU         TCGA-BR-A4IV 
"12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" 
        TCGA-BR-A4IY         TCGA-BR-A4IZ         TCGA-BR-A4J1 
"12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" 
        TCGA-BR-A4J2         TCGA-BR-A4J4         TCGA-BR-A4J5 
"12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" 
        TCGA-BR-A4J6         TCGA-BR-A4J8         TCGA-BR-A4J9 
      "12P LOSS CNV" "12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" 
        TCGA-BR-A4PF         TCGA-BR-A4QI         TCGA-BR-A4QL 
"12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" 
        TCGA-CD-5798         TCGA-CD-5799         TCGA-CD-5800 
"12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE"       "12P LOSS CNV" 
        TCGA-CD-5801         TCGA-CD-5802         TCGA-CD-5803 
"12P LOSS WILD-TYPE"       "12P LOSS CNV" "12P LOSS WILD-TYPE" 
        TCGA-CG-4300         TCGA-CG-4301         TCGA-CG-4304 
"12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" 
        TCGA-CG-4305         TCGA-CG-4306         TCGA-CG-4436 
"12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE"       "12P LOSS CNV" 
        TCGA-CG-4437         TCGA-CG-4438         TCGA-CG-4440 
"12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" 
        TCGA-CG-4441         TCGA-CG-4443         TCGA-CG-4444 
"12P LOSS WILD-TYPE"       "12P LOSS CNV" "12P LOSS WILD-TYPE" 
        TCGA-CG-4449         TCGA-CG-4455         TCGA-CG-4460 
"12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" 
        TCGA-CG-4462         TCGA-CG-4465         TCGA-CG-4466 
"12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" 
        TCGA-CG-4469         TCGA-CG-4472         TCGA-CG-4474 
"12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" 
        TCGA-CG-4477         TCGA-CG-5716         TCGA-CG-5717 
      "12P LOSS CNV" "12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" 
        TCGA-CG-5718         TCGA-CG-5719         TCGA-CG-5720 
"12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" 
        TCGA-CG-5721         TCGA-CG-5722         TCGA-CG-5723 
"12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" 
        TCGA-CG-5724         TCGA-CG-5725         TCGA-CG-5726 
"12P LOSS WILD-TYPE"       "12P LOSS CNV" "12P LOSS WILD-TYPE" 
        TCGA-CG-5727         TCGA-CG-5728         TCGA-CG-5730 
"12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" 
        TCGA-CG-5732         TCGA-CG-5733         TCGA-CG-5734 
      "12P LOSS CNV" "12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" 
        TCGA-D7-5577         TCGA-D7-5578         TCGA-D7-5579 
"12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" 
        TCGA-D7-6518         TCGA-D7-6519         TCGA-D7-6520 
"12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" 
        TCGA-D7-6521         TCGA-D7-6522         TCGA-D7-6524 
"12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" 
        TCGA-D7-6525         TCGA-D7-6526         TCGA-D7-6527 
"12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" 
        TCGA-D7-6528         TCGA-D7-6815         TCGA-D7-6817 
"12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" 
        TCGA-D7-6818         TCGA-D7-6820         TCGA-D7-6822 
"12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE"       "12P LOSS CNV" 
        TCGA-EQ-5647         TCGA-EQ-8122         TCGA-F1-6177 
"12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" 
        TCGA-F1-6874         TCGA-F1-6875         TCGA-FP-7735 
"12P LOSS WILD-TYPE"       "12P LOSS CNV" "12P LOSS WILD-TYPE" 
        TCGA-FP-7829         TCGA-FP-7916         TCGA-FP-7998 
"12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" 
        TCGA-FP-8099         TCGA-FP-8209         TCGA-FP-8210 
"12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" 
        TCGA-FP-8631         TCGA-HJ-7597         TCGA-IN-7806 
"12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" 
        TCGA-IN-7808         TCGA-IP-7968 
"12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" 
        TCGA-B7-5816         TCGA-B7-5818         TCGA-BR-6452 
"12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" 
        TCGA-BR-6455         TCGA-BR-6457         TCGA-BR-6458 
"12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" 
        TCGA-BR-6563         TCGA-BR-6564         TCGA-BR-6565 
"12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" 
        TCGA-BR-6566         TCGA-BR-6705         TCGA-BR-6706 
"12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" 
        TCGA-BR-6707         TCGA-BR-6709         TCGA-BR-6710 
"12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" 
        TCGA-BR-6801         TCGA-BR-6802         TCGA-BR-6803 
"12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" 
        TCGA-BR-6852         TCGA-BR-7196         TCGA-BR-7197 
"12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" 
        TCGA-BR-7703         TCGA-BR-7704         TCGA-BR-7707 
"12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" 
        TCGA-BR-7715         TCGA-BR-7716         TCGA-BR-7717 
      "12P LOSS CNV" "12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" 
        TCGA-BR-7722         TCGA-BR-7723         TCGA-BR-7851 
"12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" 
        TCGA-BR-7901         TCGA-BR-7957         TCGA-BR-7958 
"12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" 
        TCGA-BR-7959         TCGA-BR-8059         TCGA-BR-8060 
"12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE"       "12P LOSS CNV" 
        TCGA-BR-8077         TCGA-BR-8078         TCGA-BR-8080 
"12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" 
        TCGA-BR-8081         TCGA-BR-8284         TCGA-BR-8285 
"12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" 
        TCGA-BR-8286         TCGA-BR-8289         TCGA-BR-8291 
"12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" 
        TCGA-BR-8295         TCGA-BR-8296         TCGA-BR-8297 
"12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" 
        TCGA-BR-8592         TCGA-BR-A4IU         TCGA-BR-A4IV 
"12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" 
        TCGA-BR-A4IY         TCGA-BR-A4IZ         TCGA-BR-A4J1 
"12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" 
        TCGA-BR-A4J2         TCGA-BR-A4J4         TCGA-BR-A4J5 
"12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" 
        TCGA-BR-A4J6         TCGA-BR-A4J8         TCGA-BR-A4J9 
      "12P LOSS CNV" "12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" 
        TCGA-BR-A4PF         TCGA-BR-A4QI         TCGA-BR-A4QL 
"12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" 
        TCGA-CD-5798         TCGA-CD-5799         TCGA-CD-5800 
"12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE"       "12P LOSS CNV" 
        TCGA-CD-5801         TCGA-CD-5802         TCGA-CD-5803 
"12P LOSS WILD-TYPE"       "12P LOSS CNV" "12P LOSS WILD-TYPE" 
        TCGA-CG-4300         TCGA-CG-4301         TCGA-CG-4304 
"12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" 
        TCGA-CG-4305         TCGA-CG-4306         TCGA-CG-4436 
"12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE"       "12P LOSS CNV" 
        TCGA-CG-4437         TCGA-CG-4438         TCGA-CG-4440 
"12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" 
        TCGA-CG-4441         TCGA-CG-4443         TCGA-CG-4444 
"12P LOSS WILD-TYPE"       "12P LOSS CNV" "12P LOSS WILD-TYPE" 
        TCGA-CG-4449         TCGA-CG-4455         TCGA-CG-4460 
"12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" 
        TCGA-CG-4462         TCGA-CG-4465         TCGA-CG-4466 
"12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" 
        TCGA-CG-4469         TCGA-CG-4472         TCGA-CG-4474 
"12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" 
        TCGA-CG-4477         TCGA-CG-5716         TCGA-CG-5717 
      "12P LOSS CNV" "12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" 
        TCGA-CG-5718         TCGA-CG-5719         TCGA-CG-5720 
"12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" 
        TCGA-CG-5721         TCGA-CG-5722         TCGA-CG-5723 
"12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" 
        TCGA-CG-5724         TCGA-CG-5725         TCGA-CG-5726 
"12P LOSS WILD-TYPE"       "12P LOSS CNV" "12P LOSS WILD-TYPE" 
        TCGA-CG-5727         TCGA-CG-5728         TCGA-CG-5730 
"12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" 
        TCGA-CG-5732         TCGA-CG-5733         TCGA-CG-5734 
      "12P LOSS CNV" "12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" 
        TCGA-D7-5577         TCGA-D7-5578         TCGA-D7-5579 
"12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" 
        TCGA-D7-6518         TCGA-D7-6519         TCGA-D7-6520 
"12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" 
        TCGA-D7-6521         TCGA-D7-6522         TCGA-D7-6524 
"12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" 
        TCGA-D7-6525         TCGA-D7-6526         TCGA-D7-6527 
"12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" 
        TCGA-D7-6528         TCGA-D7-6815         TCGA-D7-6817 
"12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" 
        TCGA-D7-6818         TCGA-D7-6820         TCGA-D7-6822 
"12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE"       "12P LOSS CNV" 
        TCGA-EQ-5647         TCGA-EQ-8122         TCGA-F1-6177 
"12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" 
        TCGA-F1-6874         TCGA-F1-6875         TCGA-FP-7735 
"12P LOSS WILD-TYPE"       "12P LOSS CNV" "12P LOSS WILD-TYPE" 
        TCGA-FP-7829         TCGA-FP-7916         TCGA-FP-7998 
"12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" 
        TCGA-FP-8099         TCGA-FP-8209         TCGA-FP-8210 
"12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" 
        TCGA-FP-8631         TCGA-HJ-7597         TCGA-IN-7806 
"12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" 
        TCGA-IN-7808         TCGA-IP-7968 
"12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" 
[1] "hr=" "4.1"
D58V2, continuous
D58V3, binary
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  12P LOSS CNV          5    9
  12P LOSS WILD-TYPE   67   99
        clus
vv       12P LOSS CNV 12P LOSS WILD-TYPE
  FEMALE            5                 67
  MALE              9                 99
                    vv
clus                 STOMACH  ADENOCARCINOMA  DIFFUSE TYPE
  12P LOSS CNV                                           0
  12P LOSS WILD-TYPE                                    10
                    vv
clus                 STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  12P LOSS CNV                                                            2
  12P LOSS WILD-TYPE                                                     14
                    vv
clus                 STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  12P LOSS CNV                                                                       0
  12P LOSS WILD-TYPE                                                                 8
                    vv
clus                 STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE
  12P LOSS CNV                                                              0
  12P LOSS WILD-TYPE                                                        3
                    vv
clus                 STOMACH ADENOCARCINOMA  SIGNET RING TYPE
  12P LOSS CNV                                              0
  12P LOSS WILD-TYPE                                        1
                    vv
clus                 STOMACH ADENOCARCINOMA - DIFFUSE TYPE
  12P LOSS CNV                                           0
  12P LOSS WILD-TYPE                                    16
                    vv
clus                 STOMACH ADENOCARCINOMA - NOT OTHERWISE SPECIFIED (NOS)
  12P LOSS CNV                                                            6
  12P LOSS WILD-TYPE                                                     67
                    vv
clus                 STOMACH INTESTINAL ADENOCARCINOMA - MUCINOUS TYPE
  12P LOSS CNV                                                       0
  12P LOSS WILD-TYPE                                                 7
                    vv
clus                 STOMACH INTESTINAL ADENOCARCINOMA - PAPILLARY TYPE
  12P LOSS CNV                                                        1
  12P LOSS WILD-TYPE                                                  2
                    vv
clus                 STOMACH INTESTINAL ADENOCARCINOMA - TUBULAR TYPE
  12P LOSS CNV                                                      1
  12P LOSS WILD-TYPE                                                9
                    vv
clus                 STOMACH INTESTINAL ADENOCARCINOMA - TYPE NOT OTHERWISE SPECIFIED (NOS)
  12P LOSS CNV                                                                            4
  12P LOSS WILD-TYPE                                                                     24
D58V4, multiclass
                    vv
clus                 T1 T2 T3 T4
  12P LOSS CNV        1  7  3  0
  12P LOSS WILD-TYPE  5 45 53 18
D58V5, multiclass
    clus
vv   12P LOSS CNV 12P LOSS WILD-TYPE
  T1            1                  5
  T2            7                 45
  T3            3                 53
  T4            0                 18
                    vv
clus                 N0 N1 N2 N3
  12P LOSS CNV       10  0  0  1
  12P LOSS WILD-TYPE 34 49 23 14
D58V6, multiclass
    clus
vv   12P LOSS CNV 12P LOSS WILD-TYPE
  N0           10                 34
  N1            0                 49
  N2            0                 23
  N3            1                 14
                    vv
clus                  M0  M1  MX
  12P LOSS CNV        11   0   1
  12P LOSS WILD-TYPE 107  16   7
D58V7, multiclass
    clus
vv   12P LOSS CNV 12P LOSS WILD-TYPE
  M0           11                107
  M1            0                 16
  MX            1                  7
                    vv
clus                  I II III IV
  12P LOSS CNV        7  3   0  1
  12P LOSS WILD-TYPE 17 34  39 25
D58V8, multiclass
     clus
vv    12P LOSS CNV 12P LOSS WILD-TYPE
  I              7                 17
  II             3                 34
  III            0                 39
  IV             1                 25
D58V9, binary
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  12P LOSS CNV          1   13
  12P LOSS WILD-TYPE    4  162
     clus
vv    12P LOSS CNV 12P LOSS WILD-TYPE
  NO             1                  4
  YES           13                162
                    vv
clus                  R0  R1  R2  RX
  12P LOSS CNV        11   0   0   1
  12P LOSS WILD-TYPE 114   7  12  24
D58V10, multiclass
    clus
vv   12P LOSS CNV 12P LOSS WILD-TYPE
  R0           11                114
  R1            0                  7
  R2            0                 12
  RX            1                 24
D58V11, continuous

Clustering(59) Variable = 12q loss
D59V1, survival
                    sevent
clus2                  0   1
  12Q LOSS CNV         7   1
  12Q LOSS WILD-TYPE 117  18
      12Q LOSS CNV 12Q LOSS WILD-TYPE 
                 8                135 
      12Q LOSS CNV 12Q LOSS WILD-TYPE 
                 1                 18 
$`12Q LOSS CNV`
TCGA-BR-7715 TCGA-BR-8060 TCGA-BR-A4J6 TCGA-CD-5802 TCGA-CG-4436 TCGA-CG-4443 
        1.05         1.32         0.13         0.30        52.96        29.98 
TCGA-CG-5725 TCGA-CG-5732 
       15.02        55.04 

$`12Q LOSS WILD-TYPE`
TCGA-B7-5816 TCGA-B7-5818 TCGA-BR-6452 TCGA-BR-6455 TCGA-BR-6457 TCGA-BR-6458 
        5.62         0.10         0.95         1.41         1.35         1.35 
TCGA-BR-6563 TCGA-BR-6564 TCGA-BR-6565 TCGA-BR-6566 TCGA-BR-6705 TCGA-BR-6706 
        0.85         0.82         0.62         0.62         1.71         2.17 
TCGA-BR-6707 TCGA-BR-6709 TCGA-BR-6710 TCGA-BR-6801 TCGA-BR-6802 TCGA-BR-6803 
        0.99         1.22         0.66         1.12         0.76         0.66 
TCGA-BR-6852 TCGA-BR-7196 TCGA-BR-7197 TCGA-BR-7703 TCGA-BR-7704 TCGA-BR-7707 
        0.26         1.22         1.48         0.46         1.25         0.13 
TCGA-BR-7716 TCGA-BR-7717 TCGA-BR-7722 TCGA-BR-7723 TCGA-BR-7851 TCGA-BR-7901 
        0.82         0.69         0.16         4.54         0.99         0.95 
TCGA-BR-7957 TCGA-BR-7958 TCGA-BR-7959 TCGA-BR-8059 TCGA-BR-8077 TCGA-BR-8078 
        0.69         0.16         1.08         0.82         0.69         0.95 
TCGA-BR-8080 TCGA-BR-8081 TCGA-BR-8284 TCGA-BR-8285 TCGA-BR-8286 TCGA-BR-8289 
        0.49         0.46         0.72         0.26         0.43         0.26 
TCGA-BR-8291 TCGA-BR-8295 TCGA-BR-8296 TCGA-BR-8297 TCGA-BR-8592 TCGA-BR-A4IU 
        1.18         1.55         1.48         0.76         0.20         0.59 
TCGA-BR-A4IV TCGA-BR-A4IY TCGA-BR-A4IZ TCGA-BR-A4J1 TCGA-BR-A4J2 TCGA-BR-A4J4 
        0.92         0.39         0.79         0.72         0.79         0.53 
TCGA-BR-A4J5 TCGA-BR-A4J8 TCGA-BR-A4J9 TCGA-BR-A4PF TCGA-BR-A4QI TCGA-BR-A4QL 
        0.43         0.23         0.10         0.72         0.49         2.24 
TCGA-CD-5798 TCGA-CD-5799 TCGA-CD-5800 TCGA-CD-5801 TCGA-CD-5803 TCGA-CG-4300 
        0.82         0.69         0.36         0.49         0.07        20.02 
TCGA-CG-4301 TCGA-CG-4304 TCGA-CG-4305 TCGA-CG-4306 TCGA-CG-4437 TCGA-CG-4438 
        3.02        27.02        15.95         1.02         8.05        54.05 
TCGA-CG-4440 TCGA-CG-4441 TCGA-CG-4444 TCGA-CG-4449 TCGA-CG-4455 TCGA-CG-4460 
        4.01        14.01        47.05        19.07        12.03        21.99 
TCGA-CG-4462 TCGA-CG-4465 TCGA-CG-4466 TCGA-CG-4469 TCGA-CG-4472 TCGA-CG-4474 
        1.02         8.98        18.94         7.07        12.00         1.02 
TCGA-CG-4477 TCGA-CG-5716 TCGA-CG-5717 TCGA-CG-5718 TCGA-CG-5719 TCGA-CG-5720 
        1.02         1.02         6.94         1.02         1.02         0.99 
TCGA-CG-5721 TCGA-CG-5722 TCGA-CG-5723 TCGA-CG-5724 TCGA-CG-5726 TCGA-CG-5727 
        5.98         0.95        70.06        12.03        28.96        31.04 
TCGA-CG-5728 TCGA-CG-5730 TCGA-CG-5733 TCGA-CG-5734 TCGA-D7-5577 TCGA-D7-5578 
       65.10         4.01        21.07         7.99         8.65         3.58 
TCGA-D7-5579 TCGA-D7-6518 TCGA-D7-6519 TCGA-D7-6520 TCGA-D7-6521 TCGA-D7-6522 
        4.54         9.80        15.65         9.63         8.19         6.90 
TCGA-D7-6524 TCGA-D7-6525 TCGA-D7-6526 TCGA-D7-6527 TCGA-D7-6528 TCGA-D7-6815 
        0.69         5.95         6.61         4.14         1.68         3.65 
TCGA-D7-6817 TCGA-D7-6818 TCGA-D7-6820 TCGA-D7-6822 TCGA-EQ-5647 TCGA-EQ-8122 
        4.70         4.04         2.93         4.27         0.62         7.79 
TCGA-F1-6177 TCGA-F1-6874 TCGA-F1-6875 TCGA-FP-7735 TCGA-FP-7829 TCGA-FP-7916 
        6.54         2.01        72.23         0.39         0.20         3.02 
TCGA-FP-7998 TCGA-FP-8099 TCGA-FP-8209 TCGA-FP-8210 TCGA-FP-8631 TCGA-HJ-7597 
        3.58         1.02        59.05         5.03         0.56        26.43 
TCGA-IN-7806 TCGA-IN-7808 TCGA-IP-7968 
        6.87         3.55         2.53 

      12Q LOSS CNV 12Q LOSS WILD-TYPE 
              0.13               0.07 
      12Q LOSS CNV 12Q LOSS WILD-TYPE 
             55.04              72.23 
      12Q LOSS CNV 12Q LOSS WILD-TYPE 
              8.17               1.22 
[1] "0.1 - 55.0 (8.2)" "0.1 - 72.2 (1.2)"
        TCGA-B7-5816         TCGA-B7-5818         TCGA-BR-6452 
"12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" 
        TCGA-BR-6455         TCGA-BR-6457         TCGA-BR-6458 
"12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" 
        TCGA-BR-6563         TCGA-BR-6564         TCGA-BR-6565 
"12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" 
        TCGA-BR-6566         TCGA-BR-6705         TCGA-BR-6706 
"12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" 
        TCGA-BR-6707         TCGA-BR-6709         TCGA-BR-6710 
"12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" 
        TCGA-BR-6801         TCGA-BR-6802         TCGA-BR-6803 
"12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" 
        TCGA-BR-6852         TCGA-BR-7196         TCGA-BR-7197 
"12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" 
        TCGA-BR-7703         TCGA-BR-7704         TCGA-BR-7707 
"12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" 
        TCGA-BR-7715         TCGA-BR-7716         TCGA-BR-7717 
      "12Q LOSS CNV" "12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" 
        TCGA-BR-7722         TCGA-BR-7723         TCGA-BR-7851 
"12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" 
        TCGA-BR-7901         TCGA-BR-7957         TCGA-BR-7958 
"12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" 
        TCGA-BR-7959         TCGA-BR-8059         TCGA-BR-8060 
"12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE"       "12Q LOSS CNV" 
        TCGA-BR-8077         TCGA-BR-8078         TCGA-BR-8080 
"12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" 
        TCGA-BR-8081         TCGA-BR-8284         TCGA-BR-8285 
"12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" 
        TCGA-BR-8286         TCGA-BR-8289         TCGA-BR-8291 
"12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" 
        TCGA-BR-8295         TCGA-BR-8296         TCGA-BR-8297 
"12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" 
        TCGA-BR-8592         TCGA-BR-A4IU         TCGA-BR-A4IV 
"12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" 
        TCGA-BR-A4IY         TCGA-BR-A4IZ         TCGA-BR-A4J1 
"12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" 
        TCGA-BR-A4J2         TCGA-BR-A4J4         TCGA-BR-A4J5 
"12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" 
        TCGA-BR-A4J6         TCGA-BR-A4J8         TCGA-BR-A4J9 
      "12Q LOSS CNV" "12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" 
        TCGA-BR-A4PF         TCGA-BR-A4QI         TCGA-BR-A4QL 
"12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" 
        TCGA-CD-5798         TCGA-CD-5799         TCGA-CD-5800 
"12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" 
        TCGA-CD-5801         TCGA-CD-5802         TCGA-CD-5803 
"12Q LOSS WILD-TYPE"       "12Q LOSS CNV" "12Q LOSS WILD-TYPE" 
        TCGA-CG-4300         TCGA-CG-4301         TCGA-CG-4304 
"12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" 
        TCGA-CG-4305         TCGA-CG-4306         TCGA-CG-4436 
"12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE"       "12Q LOSS CNV" 
        TCGA-CG-4437         TCGA-CG-4438         TCGA-CG-4440 
"12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" 
        TCGA-CG-4441         TCGA-CG-4443         TCGA-CG-4444 
"12Q LOSS WILD-TYPE"       "12Q LOSS CNV" "12Q LOSS WILD-TYPE" 
        TCGA-CG-4449         TCGA-CG-4455         TCGA-CG-4460 
"12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" 
        TCGA-CG-4462         TCGA-CG-4465         TCGA-CG-4466 
"12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" 
        TCGA-CG-4469         TCGA-CG-4472         TCGA-CG-4474 
"12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" 
        TCGA-CG-4477         TCGA-CG-5716         TCGA-CG-5717 
"12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" 
        TCGA-CG-5718         TCGA-CG-5719         TCGA-CG-5720 
"12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" 
        TCGA-CG-5721         TCGA-CG-5722         TCGA-CG-5723 
"12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" 
        TCGA-CG-5724         TCGA-CG-5725         TCGA-CG-5726 
"12Q LOSS WILD-TYPE"       "12Q LOSS CNV" "12Q LOSS WILD-TYPE" 
        TCGA-CG-5727         TCGA-CG-5728         TCGA-CG-5730 
"12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" 
        TCGA-CG-5732         TCGA-CG-5733         TCGA-CG-5734 
      "12Q LOSS CNV" "12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" 
        TCGA-D7-5577         TCGA-D7-5578         TCGA-D7-5579 
"12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" 
        TCGA-D7-6518         TCGA-D7-6519         TCGA-D7-6520 
"12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" 
        TCGA-D7-6521         TCGA-D7-6522         TCGA-D7-6524 
"12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" 
        TCGA-D7-6525         TCGA-D7-6526         TCGA-D7-6527 
"12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" 
        TCGA-D7-6528         TCGA-D7-6815         TCGA-D7-6817 
"12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" 
        TCGA-D7-6818         TCGA-D7-6820         TCGA-D7-6822 
"12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" 
        TCGA-EQ-5647         TCGA-EQ-8122         TCGA-F1-6177 
"12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" 
        TCGA-F1-6874         TCGA-F1-6875         TCGA-FP-7735 
"12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" 
        TCGA-FP-7829         TCGA-FP-7916         TCGA-FP-7998 
"12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" 
        TCGA-FP-8099         TCGA-FP-8209         TCGA-FP-8210 
"12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" 
        TCGA-FP-8631         TCGA-HJ-7597         TCGA-IN-7806 
"12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" 
        TCGA-IN-7808         TCGA-IP-7968 
"12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" 
        TCGA-B7-5816         TCGA-B7-5818         TCGA-BR-6452 
"12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" 
        TCGA-BR-6455         TCGA-BR-6457         TCGA-BR-6458 
"12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" 
        TCGA-BR-6563         TCGA-BR-6564         TCGA-BR-6565 
"12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" 
        TCGA-BR-6566         TCGA-BR-6705         TCGA-BR-6706 
"12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" 
        TCGA-BR-6707         TCGA-BR-6709         TCGA-BR-6710 
"12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" 
        TCGA-BR-6801         TCGA-BR-6802         TCGA-BR-6803 
"12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" 
        TCGA-BR-6852         TCGA-BR-7196         TCGA-BR-7197 
"12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" 
        TCGA-BR-7703         TCGA-BR-7704         TCGA-BR-7707 
"12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" 
        TCGA-BR-7715         TCGA-BR-7716         TCGA-BR-7717 
      "12Q LOSS CNV" "12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" 
        TCGA-BR-7722         TCGA-BR-7723         TCGA-BR-7851 
"12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" 
        TCGA-BR-7901         TCGA-BR-7957         TCGA-BR-7958 
"12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" 
        TCGA-BR-7959         TCGA-BR-8059         TCGA-BR-8060 
"12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE"       "12Q LOSS CNV" 
        TCGA-BR-8077         TCGA-BR-8078         TCGA-BR-8080 
"12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" 
        TCGA-BR-8081         TCGA-BR-8284         TCGA-BR-8285 
"12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" 
        TCGA-BR-8286         TCGA-BR-8289         TCGA-BR-8291 
"12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" 
        TCGA-BR-8295         TCGA-BR-8296         TCGA-BR-8297 
"12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" 
        TCGA-BR-8592         TCGA-BR-A4IU         TCGA-BR-A4IV 
"12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" 
        TCGA-BR-A4IY         TCGA-BR-A4IZ         TCGA-BR-A4J1 
"12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" 
        TCGA-BR-A4J2         TCGA-BR-A4J4         TCGA-BR-A4J5 
"12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" 
        TCGA-BR-A4J6         TCGA-BR-A4J8         TCGA-BR-A4J9 
      "12Q LOSS CNV" "12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" 
        TCGA-BR-A4PF         TCGA-BR-A4QI         TCGA-BR-A4QL 
"12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" 
        TCGA-CD-5798         TCGA-CD-5799         TCGA-CD-5800 
"12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" 
        TCGA-CD-5801         TCGA-CD-5802         TCGA-CD-5803 
"12Q LOSS WILD-TYPE"       "12Q LOSS CNV" "12Q LOSS WILD-TYPE" 
        TCGA-CG-4300         TCGA-CG-4301         TCGA-CG-4304 
"12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" 
        TCGA-CG-4305         TCGA-CG-4306         TCGA-CG-4436 
"12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE"       "12Q LOSS CNV" 
        TCGA-CG-4437         TCGA-CG-4438         TCGA-CG-4440 
"12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" 
        TCGA-CG-4441         TCGA-CG-4443         TCGA-CG-4444 
"12Q LOSS WILD-TYPE"       "12Q LOSS CNV" "12Q LOSS WILD-TYPE" 
        TCGA-CG-4449         TCGA-CG-4455         TCGA-CG-4460 
"12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" 
        TCGA-CG-4462         TCGA-CG-4465         TCGA-CG-4466 
"12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" 
        TCGA-CG-4469         TCGA-CG-4472         TCGA-CG-4474 
"12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" 
        TCGA-CG-4477         TCGA-CG-5716         TCGA-CG-5717 
"12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" 
        TCGA-CG-5718         TCGA-CG-5719         TCGA-CG-5720 
"12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" 
        TCGA-CG-5721         TCGA-CG-5722         TCGA-CG-5723 
"12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" 
        TCGA-CG-5724         TCGA-CG-5725         TCGA-CG-5726 
"12Q LOSS WILD-TYPE"       "12Q LOSS CNV" "12Q LOSS WILD-TYPE" 
        TCGA-CG-5727         TCGA-CG-5728         TCGA-CG-5730 
"12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" 
        TCGA-CG-5732         TCGA-CG-5733         TCGA-CG-5734 
      "12Q LOSS CNV" "12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" 
        TCGA-D7-5577         TCGA-D7-5578         TCGA-D7-5579 
"12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" 
        TCGA-D7-6518         TCGA-D7-6519         TCGA-D7-6520 
"12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" 
        TCGA-D7-6521         TCGA-D7-6522         TCGA-D7-6524 
"12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" 
        TCGA-D7-6525         TCGA-D7-6526         TCGA-D7-6527 
"12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" 
        TCGA-D7-6528         TCGA-D7-6815         TCGA-D7-6817 
"12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" 
        TCGA-D7-6818         TCGA-D7-6820         TCGA-D7-6822 
"12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" 
        TCGA-EQ-5647         TCGA-EQ-8122         TCGA-F1-6177 
"12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" 
        TCGA-F1-6874         TCGA-F1-6875         TCGA-FP-7735 
"12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" 
        TCGA-FP-7829         TCGA-FP-7916         TCGA-FP-7998 
"12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" 
        TCGA-FP-8099         TCGA-FP-8209         TCGA-FP-8210 
"12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" 
        TCGA-FP-8631         TCGA-HJ-7597         TCGA-IN-7806 
"12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" 
        TCGA-IN-7808         TCGA-IP-7968 
"12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" 
        TCGA-B7-5816         TCGA-B7-5818         TCGA-BR-6452 
"12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" 
        TCGA-BR-6455         TCGA-BR-6457         TCGA-BR-6458 
"12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" 
        TCGA-BR-6563         TCGA-BR-6564         TCGA-BR-6565 
"12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" 
        TCGA-BR-6566         TCGA-BR-6705         TCGA-BR-6706 
"12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" 
        TCGA-BR-6707         TCGA-BR-6709         TCGA-BR-6710 
"12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" 
        TCGA-BR-6801         TCGA-BR-6802         TCGA-BR-6803 
"12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" 
        TCGA-BR-6852         TCGA-BR-7196         TCGA-BR-7197 
"12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" 
        TCGA-BR-7703         TCGA-BR-7704         TCGA-BR-7707 
"12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" 
        TCGA-BR-7715         TCGA-BR-7716         TCGA-BR-7717 
      "12Q LOSS CNV" "12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" 
        TCGA-BR-7722         TCGA-BR-7723         TCGA-BR-7851 
"12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" 
        TCGA-BR-7901         TCGA-BR-7957         TCGA-BR-7958 
"12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" 
        TCGA-BR-7959         TCGA-BR-8059         TCGA-BR-8060 
"12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE"       "12Q LOSS CNV" 
        TCGA-BR-8077         TCGA-BR-8078         TCGA-BR-8080 
"12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" 
        TCGA-BR-8081         TCGA-BR-8284         TCGA-BR-8285 
"12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" 
        TCGA-BR-8286         TCGA-BR-8289         TCGA-BR-8291 
"12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" 
        TCGA-BR-8295         TCGA-BR-8296         TCGA-BR-8297 
"12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" 
        TCGA-BR-8592         TCGA-BR-A4IU         TCGA-BR-A4IV 
"12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" 
        TCGA-BR-A4IY         TCGA-BR-A4IZ         TCGA-BR-A4J1 
"12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" 
        TCGA-BR-A4J2         TCGA-BR-A4J4         TCGA-BR-A4J5 
"12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" 
        TCGA-BR-A4J6         TCGA-BR-A4J8         TCGA-BR-A4J9 
      "12Q LOSS CNV" "12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" 
        TCGA-BR-A4PF         TCGA-BR-A4QI         TCGA-BR-A4QL 
"12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" 
        TCGA-CD-5798         TCGA-CD-5799         TCGA-CD-5800 
"12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" 
        TCGA-CD-5801         TCGA-CD-5802         TCGA-CD-5803 
"12Q LOSS WILD-TYPE"       "12Q LOSS CNV" "12Q LOSS WILD-TYPE" 
        TCGA-CG-4300         TCGA-CG-4301         TCGA-CG-4304 
"12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" 
        TCGA-CG-4305         TCGA-CG-4306         TCGA-CG-4436 
"12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE"       "12Q LOSS CNV" 
        TCGA-CG-4437         TCGA-CG-4438         TCGA-CG-4440 
"12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" 
        TCGA-CG-4441         TCGA-CG-4443         TCGA-CG-4444 
"12Q LOSS WILD-TYPE"       "12Q LOSS CNV" "12Q LOSS WILD-TYPE" 
        TCGA-CG-4449         TCGA-CG-4455         TCGA-CG-4460 
"12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" 
        TCGA-CG-4462         TCGA-CG-4465         TCGA-CG-4466 
"12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" 
        TCGA-CG-4469         TCGA-CG-4472         TCGA-CG-4474 
"12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" 
        TCGA-CG-4477         TCGA-CG-5716         TCGA-CG-5717 
"12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" 
        TCGA-CG-5718         TCGA-CG-5719         TCGA-CG-5720 
"12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" 
        TCGA-CG-5721         TCGA-CG-5722         TCGA-CG-5723 
"12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" 
        TCGA-CG-5724         TCGA-CG-5725         TCGA-CG-5726 
"12Q LOSS WILD-TYPE"       "12Q LOSS CNV" "12Q LOSS WILD-TYPE" 
        TCGA-CG-5727         TCGA-CG-5728         TCGA-CG-5730 
"12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" 
        TCGA-CG-5732         TCGA-CG-5733         TCGA-CG-5734 
      "12Q LOSS CNV" "12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" 
        TCGA-D7-5577         TCGA-D7-5578         TCGA-D7-5579 
"12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" 
        TCGA-D7-6518         TCGA-D7-6519         TCGA-D7-6520 
"12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" 
        TCGA-D7-6521         TCGA-D7-6522         TCGA-D7-6524 
"12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" 
        TCGA-D7-6525         TCGA-D7-6526         TCGA-D7-6527 
"12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" 
        TCGA-D7-6528         TCGA-D7-6815         TCGA-D7-6817 
"12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" 
        TCGA-D7-6818         TCGA-D7-6820         TCGA-D7-6822 
"12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" 
        TCGA-EQ-5647         TCGA-EQ-8122         TCGA-F1-6177 
"12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" 
        TCGA-F1-6874         TCGA-F1-6875         TCGA-FP-7735 
"12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" 
        TCGA-FP-7829         TCGA-FP-7916         TCGA-FP-7998 
"12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" 
        TCGA-FP-8099         TCGA-FP-8209         TCGA-FP-8210 
"12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" 
        TCGA-FP-8631         TCGA-HJ-7597         TCGA-IN-7806 
"12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" 
        TCGA-IN-7808         TCGA-IP-7968 
"12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" 
[1] "hr=" "2.7"
D59V2, continuous
D59V3, binary
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  12Q LOSS CNV          2    7
  12Q LOSS WILD-TYPE   70  101
        clus
vv       12Q LOSS CNV 12Q LOSS WILD-TYPE
  FEMALE            2                 70
  MALE              7                101
                    vv
clus                 STOMACH  ADENOCARCINOMA  DIFFUSE TYPE
  12Q LOSS CNV                                           0
  12Q LOSS WILD-TYPE                                    10
                    vv
clus                 STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  12Q LOSS CNV                                                            2
  12Q LOSS WILD-TYPE                                                     14
                    vv
clus                 STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  12Q LOSS CNV                                                                       0
  12Q LOSS WILD-TYPE                                                                 8
                    vv
clus                 STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE
  12Q LOSS CNV                                                              0
  12Q LOSS WILD-TYPE                                                        3
                    vv
clus                 STOMACH ADENOCARCINOMA  SIGNET RING TYPE
  12Q LOSS CNV                                              0
  12Q LOSS WILD-TYPE                                        1
                    vv
clus                 STOMACH ADENOCARCINOMA - DIFFUSE TYPE
  12Q LOSS CNV                                           0
  12Q LOSS WILD-TYPE                                    16
                    vv
clus                 STOMACH ADENOCARCINOMA - NOT OTHERWISE SPECIFIED (NOS)
  12Q LOSS CNV                                                            4
  12Q LOSS WILD-TYPE                                                     69
                    vv
clus                 STOMACH INTESTINAL ADENOCARCINOMA - MUCINOUS TYPE
  12Q LOSS CNV                                                       0
  12Q LOSS WILD-TYPE                                                 7
                    vv
clus                 STOMACH INTESTINAL ADENOCARCINOMA - PAPILLARY TYPE
  12Q LOSS CNV                                                        0
  12Q LOSS WILD-TYPE                                                  3
                    vv
clus                 STOMACH INTESTINAL ADENOCARCINOMA - TUBULAR TYPE
  12Q LOSS CNV                                                      0
  12Q LOSS WILD-TYPE                                               10
                    vv
clus                 STOMACH INTESTINAL ADENOCARCINOMA - TYPE NOT OTHERWISE SPECIFIED (NOS)
  12Q LOSS CNV                                                                            3
  12Q LOSS WILD-TYPE                                                                     25
D59V4, multiclass
                    vv
clus                 T1 T2 T3 T4
  12Q LOSS CNV        1  3  2  0
  12Q LOSS WILD-TYPE  5 49 54 18
D59V5, multiclass
    clus
vv   12Q LOSS CNV 12Q LOSS WILD-TYPE
  T1            1                  5
  T2            3                 49
  T3            2                 54
  T4            0                 18
                    vv
clus                 N0 N1 N2 N3
  12Q LOSS CNV        5  0  0  1
  12Q LOSS WILD-TYPE 39 49 23 14
D59V6, multiclass
    clus
vv   12Q LOSS CNV 12Q LOSS WILD-TYPE
  N0            5                 39
  N1            0                 49
  N2            0                 23
  N3            1                 14
                    vv
clus                  M0  M1  MX
  12Q LOSS CNV         7   0   0
  12Q LOSS WILD-TYPE 111  16   8
D59V7, multiclass
    clus
vv   12Q LOSS CNV 12Q LOSS WILD-TYPE
  M0            7                111
  M1            0                 16
  MX            0                  8
                    vv
clus                  I II III IV
  12Q LOSS CNV        3  2   0  1
  12Q LOSS WILD-TYPE 21 35  39 25
D59V8, multiclass
     clus
vv    12Q LOSS CNV 12Q LOSS WILD-TYPE
  I              3                 21
  II             2                 35
  III            0                 39
  IV             1                 25
D59V9, binary
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  12Q LOSS CNV          0    9
  12Q LOSS WILD-TYPE    5  166
     clus
vv    12Q LOSS CNV 12Q LOSS WILD-TYPE
  NO             0                  5
  YES            9                166
                    vv
clus                  R0  R1  R2  RX
  12Q LOSS CNV         7   0   0   1
  12Q LOSS WILD-TYPE 118   7  12  24
D59V10, multiclass
    clus
vv   12Q LOSS CNV 12Q LOSS WILD-TYPE
  R0            7                118
  R1            0                  7
  R2            0                 12
  RX            1                 24
D59V11, continuous

Clustering(60) Variable = 13q loss
D60V1, survival
                    sevent
clus2                  0   1
  13Q LOSS CNV         2   0
  13Q LOSS WILD-TYPE 122  19
      13Q LOSS CNV 13Q LOSS WILD-TYPE 
                 2                141 
      13Q LOSS CNV 13Q LOSS WILD-TYPE 
                 0                 19 
$`13Q LOSS CNV`
TCGA-CG-4301 TCGA-D7-6525 
        3.02         5.95 

$`13Q LOSS WILD-TYPE`
TCGA-B7-5816 TCGA-B7-5818 TCGA-BR-6452 TCGA-BR-6455 TCGA-BR-6457 TCGA-BR-6458 
        5.62         0.10         0.95         1.41         1.35         1.35 
TCGA-BR-6563 TCGA-BR-6564 TCGA-BR-6565 TCGA-BR-6566 TCGA-BR-6705 TCGA-BR-6706 
        0.85         0.82         0.62         0.62         1.71         2.17 
TCGA-BR-6707 TCGA-BR-6709 TCGA-BR-6710 TCGA-BR-6801 TCGA-BR-6802 TCGA-BR-6803 
        0.99         1.22         0.66         1.12         0.76         0.66 
TCGA-BR-6852 TCGA-BR-7196 TCGA-BR-7197 TCGA-BR-7703 TCGA-BR-7704 TCGA-BR-7707 
        0.26         1.22         1.48         0.46         1.25         0.13 
TCGA-BR-7715 TCGA-BR-7716 TCGA-BR-7717 TCGA-BR-7722 TCGA-BR-7723 TCGA-BR-7851 
        1.05         0.82         0.69         0.16         4.54         0.99 
TCGA-BR-7901 TCGA-BR-7957 TCGA-BR-7958 TCGA-BR-7959 TCGA-BR-8059 TCGA-BR-8060 
        0.95         0.69         0.16         1.08         0.82         1.32 
TCGA-BR-8077 TCGA-BR-8078 TCGA-BR-8080 TCGA-BR-8081 TCGA-BR-8284 TCGA-BR-8285 
        0.69         0.95         0.49         0.46         0.72         0.26 
TCGA-BR-8286 TCGA-BR-8289 TCGA-BR-8291 TCGA-BR-8295 TCGA-BR-8296 TCGA-BR-8297 
        0.43         0.26         1.18         1.55         1.48         0.76 
TCGA-BR-8592 TCGA-BR-A4IU TCGA-BR-A4IV TCGA-BR-A4IY TCGA-BR-A4IZ TCGA-BR-A4J1 
        0.20         0.59         0.92         0.39         0.79         0.72 
TCGA-BR-A4J2 TCGA-BR-A4J4 TCGA-BR-A4J5 TCGA-BR-A4J6 TCGA-BR-A4J8 TCGA-BR-A4J9 
        0.79         0.53         0.43         0.13         0.23         0.10 
TCGA-BR-A4PF TCGA-BR-A4QI TCGA-BR-A4QL TCGA-CD-5798 TCGA-CD-5799 TCGA-CD-5800 
        0.72         0.49         2.24         0.82         0.69         0.36 
TCGA-CD-5801 TCGA-CD-5802 TCGA-CD-5803 TCGA-CG-4300 TCGA-CG-4304 TCGA-CG-4305 
        0.49         0.30         0.07        20.02        27.02        15.95 
TCGA-CG-4306 TCGA-CG-4436 TCGA-CG-4437 TCGA-CG-4438 TCGA-CG-4440 TCGA-CG-4441 
        1.02        52.96         8.05        54.05         4.01        14.01 
TCGA-CG-4443 TCGA-CG-4444 TCGA-CG-4449 TCGA-CG-4455 TCGA-CG-4460 TCGA-CG-4462 
       29.98        47.05        19.07        12.03        21.99         1.02 
TCGA-CG-4465 TCGA-CG-4466 TCGA-CG-4469 TCGA-CG-4472 TCGA-CG-4474 TCGA-CG-4477 
        8.98        18.94         7.07        12.00         1.02         1.02 
TCGA-CG-5716 TCGA-CG-5717 TCGA-CG-5718 TCGA-CG-5719 TCGA-CG-5720 TCGA-CG-5721 
        1.02         6.94         1.02         1.02         0.99         5.98 
TCGA-CG-5722 TCGA-CG-5723 TCGA-CG-5724 TCGA-CG-5725 TCGA-CG-5726 TCGA-CG-5727 
        0.95        70.06        12.03        15.02        28.96        31.04 
TCGA-CG-5728 TCGA-CG-5730 TCGA-CG-5732 TCGA-CG-5733 TCGA-CG-5734 TCGA-D7-5577 
       65.10         4.01        55.04        21.07         7.99         8.65 
TCGA-D7-5578 TCGA-D7-5579 TCGA-D7-6518 TCGA-D7-6519 TCGA-D7-6520 TCGA-D7-6521 
        3.58         4.54         9.80        15.65         9.63         8.19 
TCGA-D7-6522 TCGA-D7-6524 TCGA-D7-6526 TCGA-D7-6527 TCGA-D7-6528 TCGA-D7-6815 
        6.90         0.69         6.61         4.14         1.68         3.65 
TCGA-D7-6817 TCGA-D7-6818 TCGA-D7-6820 TCGA-D7-6822 TCGA-EQ-5647 TCGA-EQ-8122 
        4.70         4.04         2.93         4.27         0.62         7.79 
TCGA-F1-6177 TCGA-F1-6874 TCGA-F1-6875 TCGA-FP-7735 TCGA-FP-7829 TCGA-FP-7916 
        6.54         2.01        72.23         0.39         0.20         3.02 
TCGA-FP-7998 TCGA-FP-8099 TCGA-FP-8209 TCGA-FP-8210 TCGA-FP-8631 TCGA-HJ-7597 
        3.58         1.02        59.05         5.03         0.56        26.43 
TCGA-IN-7806 TCGA-IN-7808 TCGA-IP-7968 
        6.87         3.55         2.53 

      13Q LOSS CNV 13Q LOSS WILD-TYPE 
              3.02               0.07 
      13Q LOSS CNV 13Q LOSS WILD-TYPE 
              5.95              72.23 
      13Q LOSS CNV 13Q LOSS WILD-TYPE 
             4.485              1.220 
[1] "3.0 - 6.0 (4.5)"  "0.1 - 72.2 (1.2)"
        TCGA-B7-5816         TCGA-B7-5818         TCGA-BR-6452 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-BR-6455         TCGA-BR-6457         TCGA-BR-6458 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-BR-6563         TCGA-BR-6564         TCGA-BR-6565 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-BR-6566         TCGA-BR-6705         TCGA-BR-6706 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-BR-6707         TCGA-BR-6709         TCGA-BR-6710 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-BR-6801         TCGA-BR-6802         TCGA-BR-6803 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-BR-6852         TCGA-BR-7196         TCGA-BR-7197 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-BR-7703         TCGA-BR-7704         TCGA-BR-7707 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-BR-7715         TCGA-BR-7716         TCGA-BR-7717 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-BR-7722         TCGA-BR-7723         TCGA-BR-7851 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-BR-7901         TCGA-BR-7957         TCGA-BR-7958 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-BR-7959         TCGA-BR-8059         TCGA-BR-8060 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-BR-8077         TCGA-BR-8078         TCGA-BR-8080 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-BR-8081         TCGA-BR-8284         TCGA-BR-8285 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-BR-8286         TCGA-BR-8289         TCGA-BR-8291 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-BR-8295         TCGA-BR-8296         TCGA-BR-8297 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-BR-8592         TCGA-BR-A4IU         TCGA-BR-A4IV 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-BR-A4IY         TCGA-BR-A4IZ         TCGA-BR-A4J1 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-BR-A4J2         TCGA-BR-A4J4         TCGA-BR-A4J5 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-BR-A4J6         TCGA-BR-A4J8         TCGA-BR-A4J9 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-BR-A4PF         TCGA-BR-A4QI         TCGA-BR-A4QL 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-CD-5798         TCGA-CD-5799         TCGA-CD-5800 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-CD-5801         TCGA-CD-5802         TCGA-CD-5803 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-CG-4300         TCGA-CG-4301         TCGA-CG-4304 
"13Q LOSS WILD-TYPE"       "13Q LOSS CNV" "13Q LOSS WILD-TYPE" 
        TCGA-CG-4305         TCGA-CG-4306         TCGA-CG-4436 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-CG-4437         TCGA-CG-4438         TCGA-CG-4440 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-CG-4441         TCGA-CG-4443         TCGA-CG-4444 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-CG-4449         TCGA-CG-4455         TCGA-CG-4460 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-CG-4462         TCGA-CG-4465         TCGA-CG-4466 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-CG-4469         TCGA-CG-4472         TCGA-CG-4474 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-CG-4477         TCGA-CG-5716         TCGA-CG-5717 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-CG-5718         TCGA-CG-5719         TCGA-CG-5720 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-CG-5721         TCGA-CG-5722         TCGA-CG-5723 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-CG-5724         TCGA-CG-5725         TCGA-CG-5726 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-CG-5727         TCGA-CG-5728         TCGA-CG-5730 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-CG-5732         TCGA-CG-5733         TCGA-CG-5734 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-D7-5577         TCGA-D7-5578         TCGA-D7-5579 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-D7-6518         TCGA-D7-6519         TCGA-D7-6520 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-D7-6521         TCGA-D7-6522         TCGA-D7-6524 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-D7-6525         TCGA-D7-6526         TCGA-D7-6527 
      "13Q LOSS CNV" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-D7-6528         TCGA-D7-6815         TCGA-D7-6817 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-D7-6818         TCGA-D7-6820         TCGA-D7-6822 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-EQ-5647         TCGA-EQ-8122         TCGA-F1-6177 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-F1-6874         TCGA-F1-6875         TCGA-FP-7735 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-FP-7829         TCGA-FP-7916         TCGA-FP-7998 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-FP-8099         TCGA-FP-8209         TCGA-FP-8210 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-FP-8631         TCGA-HJ-7597         TCGA-IN-7806 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-IN-7808         TCGA-IP-7968 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-B7-5816         TCGA-B7-5818         TCGA-BR-6452 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-BR-6455         TCGA-BR-6457         TCGA-BR-6458 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-BR-6563         TCGA-BR-6564         TCGA-BR-6565 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-BR-6566         TCGA-BR-6705         TCGA-BR-6706 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-BR-6707         TCGA-BR-6709         TCGA-BR-6710 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-BR-6801         TCGA-BR-6802         TCGA-BR-6803 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-BR-6852         TCGA-BR-7196         TCGA-BR-7197 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-BR-7703         TCGA-BR-7704         TCGA-BR-7707 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-BR-7715         TCGA-BR-7716         TCGA-BR-7717 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-BR-7722         TCGA-BR-7723         TCGA-BR-7851 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-BR-7901         TCGA-BR-7957         TCGA-BR-7958 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-BR-7959         TCGA-BR-8059         TCGA-BR-8060 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-BR-8077         TCGA-BR-8078         TCGA-BR-8080 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-BR-8081         TCGA-BR-8284         TCGA-BR-8285 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-BR-8286         TCGA-BR-8289         TCGA-BR-8291 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-BR-8295         TCGA-BR-8296         TCGA-BR-8297 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-BR-8592         TCGA-BR-A4IU         TCGA-BR-A4IV 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-BR-A4IY         TCGA-BR-A4IZ         TCGA-BR-A4J1 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-BR-A4J2         TCGA-BR-A4J4         TCGA-BR-A4J5 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-BR-A4J6         TCGA-BR-A4J8         TCGA-BR-A4J9 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-BR-A4PF         TCGA-BR-A4QI         TCGA-BR-A4QL 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-CD-5798         TCGA-CD-5799         TCGA-CD-5800 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-CD-5801         TCGA-CD-5802         TCGA-CD-5803 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-CG-4300         TCGA-CG-4301         TCGA-CG-4304 
"13Q LOSS WILD-TYPE"       "13Q LOSS CNV" "13Q LOSS WILD-TYPE" 
        TCGA-CG-4305         TCGA-CG-4306         TCGA-CG-4436 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-CG-4437         TCGA-CG-4438         TCGA-CG-4440 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-CG-4441         TCGA-CG-4443         TCGA-CG-4444 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-CG-4449         TCGA-CG-4455         TCGA-CG-4460 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-CG-4462         TCGA-CG-4465         TCGA-CG-4466 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-CG-4469         TCGA-CG-4472         TCGA-CG-4474 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-CG-4477         TCGA-CG-5716         TCGA-CG-5717 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-CG-5718         TCGA-CG-5719         TCGA-CG-5720 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-CG-5721         TCGA-CG-5722         TCGA-CG-5723 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-CG-5724         TCGA-CG-5725         TCGA-CG-5726 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-CG-5727         TCGA-CG-5728         TCGA-CG-5730 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-CG-5732         TCGA-CG-5733         TCGA-CG-5734 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-D7-5577         TCGA-D7-5578         TCGA-D7-5579 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-D7-6518         TCGA-D7-6519         TCGA-D7-6520 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-D7-6521         TCGA-D7-6522         TCGA-D7-6524 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-D7-6525         TCGA-D7-6526         TCGA-D7-6527 
      "13Q LOSS CNV" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-D7-6528         TCGA-D7-6815         TCGA-D7-6817 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-D7-6818         TCGA-D7-6820         TCGA-D7-6822 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-EQ-5647         TCGA-EQ-8122         TCGA-F1-6177 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-F1-6874         TCGA-F1-6875         TCGA-FP-7735 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-FP-7829         TCGA-FP-7916         TCGA-FP-7998 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-FP-8099         TCGA-FP-8209         TCGA-FP-8210 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-FP-8631         TCGA-HJ-7597         TCGA-IN-7806 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-IN-7808         TCGA-IP-7968 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-B7-5816         TCGA-B7-5818         TCGA-BR-6452 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-BR-6455         TCGA-BR-6457         TCGA-BR-6458 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-BR-6563         TCGA-BR-6564         TCGA-BR-6565 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-BR-6566         TCGA-BR-6705         TCGA-BR-6706 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-BR-6707         TCGA-BR-6709         TCGA-BR-6710 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-BR-6801         TCGA-BR-6802         TCGA-BR-6803 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-BR-6852         TCGA-BR-7196         TCGA-BR-7197 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-BR-7703         TCGA-BR-7704         TCGA-BR-7707 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-BR-7715         TCGA-BR-7716         TCGA-BR-7717 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-BR-7722         TCGA-BR-7723         TCGA-BR-7851 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-BR-7901         TCGA-BR-7957         TCGA-BR-7958 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-BR-7959         TCGA-BR-8059         TCGA-BR-8060 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-BR-8077         TCGA-BR-8078         TCGA-BR-8080 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-BR-8081         TCGA-BR-8284         TCGA-BR-8285 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-BR-8286         TCGA-BR-8289         TCGA-BR-8291 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-BR-8295         TCGA-BR-8296         TCGA-BR-8297 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-BR-8592         TCGA-BR-A4IU         TCGA-BR-A4IV 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-BR-A4IY         TCGA-BR-A4IZ         TCGA-BR-A4J1 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-BR-A4J2         TCGA-BR-A4J4         TCGA-BR-A4J5 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-BR-A4J6         TCGA-BR-A4J8         TCGA-BR-A4J9 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-BR-A4PF         TCGA-BR-A4QI         TCGA-BR-A4QL 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-CD-5798         TCGA-CD-5799         TCGA-CD-5800 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-CD-5801         TCGA-CD-5802         TCGA-CD-5803 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-CG-4300         TCGA-CG-4301         TCGA-CG-4304 
"13Q LOSS WILD-TYPE"       "13Q LOSS CNV" "13Q LOSS WILD-TYPE" 
        TCGA-CG-4305         TCGA-CG-4306         TCGA-CG-4436 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-CG-4437         TCGA-CG-4438         TCGA-CG-4440 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-CG-4441         TCGA-CG-4443         TCGA-CG-4444 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-CG-4449         TCGA-CG-4455         TCGA-CG-4460 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-CG-4462         TCGA-CG-4465         TCGA-CG-4466 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-CG-4469         TCGA-CG-4472         TCGA-CG-4474 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-CG-4477         TCGA-CG-5716         TCGA-CG-5717 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-CG-5718         TCGA-CG-5719         TCGA-CG-5720 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-CG-5721         TCGA-CG-5722         TCGA-CG-5723 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-CG-5724         TCGA-CG-5725         TCGA-CG-5726 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-CG-5727         TCGA-CG-5728         TCGA-CG-5730 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-CG-5732         TCGA-CG-5733         TCGA-CG-5734 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-D7-5577         TCGA-D7-5578         TCGA-D7-5579 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-D7-6518         TCGA-D7-6519         TCGA-D7-6520 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-D7-6521         TCGA-D7-6522         TCGA-D7-6524 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-D7-6525         TCGA-D7-6526         TCGA-D7-6527 
      "13Q LOSS CNV" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-D7-6528         TCGA-D7-6815         TCGA-D7-6817 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-D7-6818         TCGA-D7-6820         TCGA-D7-6822 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-EQ-5647         TCGA-EQ-8122         TCGA-F1-6177 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-F1-6874         TCGA-F1-6875         TCGA-FP-7735 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-FP-7829         TCGA-FP-7916         TCGA-FP-7998 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-FP-8099         TCGA-FP-8209         TCGA-FP-8210 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-FP-8631         TCGA-HJ-7597         TCGA-IN-7806 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-IN-7808         TCGA-IP-7968 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
[1] "Remove cluster labels:" "13Q LOSS CNV"          
clus
      13Q LOSS CNV 13Q LOSS WILD-TYPE 
                 2                141 
        TCGA-B7-5816         TCGA-B7-5818         TCGA-BR-6452 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-BR-6455         TCGA-BR-6457         TCGA-BR-6458 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-BR-6563         TCGA-BR-6564         TCGA-BR-6565 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-BR-6566         TCGA-BR-6705         TCGA-BR-6706 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-BR-6707         TCGA-BR-6709         TCGA-BR-6710 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-BR-6801         TCGA-BR-6802         TCGA-BR-6803 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-BR-6852         TCGA-BR-7196         TCGA-BR-7197 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-BR-7703         TCGA-BR-7704         TCGA-BR-7707 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-BR-7715         TCGA-BR-7716         TCGA-BR-7717 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-BR-7722         TCGA-BR-7723         TCGA-BR-7851 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-BR-7901         TCGA-BR-7957         TCGA-BR-7958 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-BR-7959         TCGA-BR-8059         TCGA-BR-8060 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-BR-8077         TCGA-BR-8078         TCGA-BR-8080 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-BR-8081         TCGA-BR-8284         TCGA-BR-8285 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-BR-8286         TCGA-BR-8289         TCGA-BR-8291 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-BR-8295         TCGA-BR-8296         TCGA-BR-8297 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-BR-8592         TCGA-BR-A4IU         TCGA-BR-A4IV 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-BR-A4IY         TCGA-BR-A4IZ         TCGA-BR-A4J1 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-BR-A4J2         TCGA-BR-A4J4         TCGA-BR-A4J5 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-BR-A4J6         TCGA-BR-A4J8         TCGA-BR-A4J9 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-BR-A4PF         TCGA-BR-A4QI         TCGA-BR-A4QL 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-CD-5798         TCGA-CD-5799         TCGA-CD-5800 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-CD-5801         TCGA-CD-5802         TCGA-CD-5803 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-CG-4300         TCGA-CG-4304         TCGA-CG-4305 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-CG-4306         TCGA-CG-4436         TCGA-CG-4437 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-CG-4438         TCGA-CG-4440         TCGA-CG-4441 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-CG-4443         TCGA-CG-4444         TCGA-CG-4449 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-CG-4455         TCGA-CG-4460         TCGA-CG-4462 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-CG-4465         TCGA-CG-4466         TCGA-CG-4469 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-CG-4472         TCGA-CG-4474         TCGA-CG-4477 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-CG-5716         TCGA-CG-5717         TCGA-CG-5718 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-CG-5719         TCGA-CG-5720         TCGA-CG-5721 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-CG-5722         TCGA-CG-5723         TCGA-CG-5724 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-CG-5725         TCGA-CG-5726         TCGA-CG-5727 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-CG-5728         TCGA-CG-5730         TCGA-CG-5732 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-CG-5733         TCGA-CG-5734         TCGA-D7-5577 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-D7-5578         TCGA-D7-5579         TCGA-D7-6518 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-D7-6519         TCGA-D7-6520         TCGA-D7-6521 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-D7-6522         TCGA-D7-6524         TCGA-D7-6526 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-D7-6527         TCGA-D7-6528         TCGA-D7-6815 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-D7-6817         TCGA-D7-6818         TCGA-D7-6820 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-D7-6822         TCGA-EQ-5647         TCGA-EQ-8122 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-F1-6177         TCGA-F1-6874         TCGA-F1-6875 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-FP-7735         TCGA-FP-7829         TCGA-FP-7916 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-FP-7998         TCGA-FP-8099         TCGA-FP-8209 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-FP-8210         TCGA-FP-8631         TCGA-HJ-7597 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-IN-7806         TCGA-IN-7808         TCGA-IP-7968 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
D60V2, continuous
D60V3, binary
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  13Q LOSS CNV          2    3
  13Q LOSS WILD-TYPE   70  105
        clus
vv       13Q LOSS CNV 13Q LOSS WILD-TYPE
  FEMALE            2                 70
  MALE              3                105
                    vv
clus                 STOMACH  ADENOCARCINOMA  DIFFUSE TYPE
  13Q LOSS CNV                                           0
  13Q LOSS WILD-TYPE                                    10
                    vv
clus                 STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  13Q LOSS CNV                                                            0
  13Q LOSS WILD-TYPE                                                     16
                    vv
clus                 STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  13Q LOSS CNV                                                                       0
  13Q LOSS WILD-TYPE                                                                 8
                    vv
clus                 STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE
  13Q LOSS CNV                                                              0
  13Q LOSS WILD-TYPE                                                        3
                    vv
clus                 STOMACH ADENOCARCINOMA  SIGNET RING TYPE
  13Q LOSS CNV                                              0
  13Q LOSS WILD-TYPE                                        1
                    vv
clus                 STOMACH ADENOCARCINOMA - DIFFUSE TYPE
  13Q LOSS CNV                                           1
  13Q LOSS WILD-TYPE                                    15
                    vv
clus                 STOMACH ADENOCARCINOMA - NOT OTHERWISE SPECIFIED (NOS)
  13Q LOSS CNV                                                            1
  13Q LOSS WILD-TYPE                                                     72
                    vv
clus                 STOMACH INTESTINAL ADENOCARCINOMA - MUCINOUS TYPE
  13Q LOSS CNV                                                       1
  13Q LOSS WILD-TYPE                                                 6
                    vv
clus                 STOMACH INTESTINAL ADENOCARCINOMA - PAPILLARY TYPE
  13Q LOSS CNV                                                        0
  13Q LOSS WILD-TYPE                                                  3
                    vv
clus                 STOMACH INTESTINAL ADENOCARCINOMA - TUBULAR TYPE
  13Q LOSS CNV                                                      1
  13Q LOSS WILD-TYPE                                                9
                    vv
clus                 STOMACH INTESTINAL ADENOCARCINOMA - TYPE NOT OTHERWISE SPECIFIED (NOS)
  13Q LOSS CNV                                                                            0
  13Q LOSS WILD-TYPE                                                                     28
D60V4, multiclass
                    vv
clus                 T1 T2 T3 T4
  13Q LOSS CNV        0  3  1  1
  13Q LOSS WILD-TYPE  6 49 55 17
D60V5, multiclass
    clus
vv   13Q LOSS CNV 13Q LOSS WILD-TYPE
  T1            0                  6
  T2            3                 49
  T3            1                 55
  T4            1                 17
                    vv
clus                 N0 N1 N2 N3
  13Q LOSS CNV        0  2  1  1
  13Q LOSS WILD-TYPE 44 47 22 14
D60V6, multiclass
    clus
vv   13Q LOSS CNV 13Q LOSS WILD-TYPE
  N0            0                 44
  N1            2                 47
  N2            1                 22
  N3            1                 14
                    vv
clus                  M0  M1  MX
  13Q LOSS CNV         4   1   0
  13Q LOSS WILD-TYPE 114  15   8
D60V7, multiclass
    clus
vv   13Q LOSS CNV 13Q LOSS WILD-TYPE
  M0            4                114
  M1            1                 15
  MX            0                  8
                    vv
clus                  I II III IV
  13Q LOSS CNV        0  1   1  2
  13Q LOSS WILD-TYPE 24 36  38 24
D60V8, multiclass
     clus
vv    13Q LOSS CNV 13Q LOSS WILD-TYPE
  I              0                 24
  II             1                 36
  III            1                 38
  IV             2                 24
D60V9, binary
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  13Q LOSS CNV          1    4
  13Q LOSS WILD-TYPE    4  171
     clus
vv    13Q LOSS CNV 13Q LOSS WILD-TYPE
  NO             1                  4
  YES            4                171
                    vv
clus                  R0  R1  R2  RX
  13Q LOSS CNV         2   1   1   1
  13Q LOSS WILD-TYPE 123   6  11  24
D60V10, multiclass
    clus
vv   13Q LOSS CNV 13Q LOSS WILD-TYPE
  R0            2                123
  R1            1                  6
  R2            1                 11
  RX            1                 24
D60V11, continuous
[1] "Remove cluster labels:" "13Q LOSS CNV"          
clus
      13Q LOSS CNV 13Q LOSS WILD-TYPE 
                 2                134 
        TCGA-B7-5816         TCGA-BR-4183         TCGA-BR-4184 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-BR-4188         TCGA-BR-4191         TCGA-BR-4253 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-BR-4255         TCGA-BR-4256         TCGA-BR-4267 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-BR-4279         TCGA-BR-4280         TCGA-BR-4361 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-BR-4362         TCGA-BR-4367         TCGA-BR-4368 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-BR-6452         TCGA-BR-6453         TCGA-BR-6454 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-BR-6455         TCGA-BR-6456         TCGA-BR-6457 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-BR-6458         TCGA-BR-6563         TCGA-BR-6564 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-BR-6565         TCGA-BR-6566         TCGA-BR-6705 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-BR-6706         TCGA-BR-6707         TCGA-BR-6709 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-BR-6710         TCGA-BR-6801         TCGA-BR-6802 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-BR-6803         TCGA-BR-6852         TCGA-BR-7196 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-BR-7197         TCGA-BR-7703         TCGA-BR-7704 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-BR-7707         TCGA-BR-7715         TCGA-BR-7716 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-BR-7717         TCGA-BR-7722         TCGA-BR-7723 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-BR-7851         TCGA-BR-7901         TCGA-BR-7957 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-BR-7958         TCGA-BR-7959         TCGA-BR-8059 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-BR-8060         TCGA-BR-8077         TCGA-BR-8078 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-BR-8080         TCGA-BR-8081         TCGA-BR-8284 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-BR-8285         TCGA-BR-8286         TCGA-BR-8289 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-BR-8291         TCGA-BR-8295         TCGA-BR-8296 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-BR-8297         TCGA-BR-8592         TCGA-BR-A4IU 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-BR-A4IV         TCGA-BR-A4IY         TCGA-BR-A4IZ 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-BR-A4J1         TCGA-BR-A4J2         TCGA-BR-A4J4 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-BR-A4J5         TCGA-BR-A4J6         TCGA-BR-A4J8 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-BR-A4J9         TCGA-BR-A4PF         TCGA-BR-A4QI 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-BR-A4QL         TCGA-CD-5804         TCGA-CG-5717 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-CG-5718         TCGA-CG-5719         TCGA-CG-5720 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-CG-5721         TCGA-CG-5722         TCGA-CG-5723 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-CG-5724         TCGA-CG-5725         TCGA-CG-5726 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-CG-5727         TCGA-CG-5728         TCGA-CG-5730 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-CG-5732         TCGA-CG-5733         TCGA-CG-5734 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-D7-5577         TCGA-D7-5578         TCGA-D7-5579 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-D7-6518         TCGA-D7-6519         TCGA-D7-6520 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-D7-6521         TCGA-D7-6522         TCGA-D7-6524 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-D7-6526         TCGA-D7-6527         TCGA-D7-6528 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-D7-6815         TCGA-D7-6817         TCGA-D7-6818 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-D7-6820         TCGA-D7-6822         TCGA-EQ-5647 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-EQ-8122         TCGA-F1-6177         TCGA-F1-6874 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-F1-6875         TCGA-FP-7735         TCGA-FP-7829 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-FP-7916         TCGA-FP-7998         TCGA-FP-8099 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-FP-8209         TCGA-FP-8210         TCGA-FP-8631 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-HF-7131         TCGA-HF-7132         TCGA-HF-7134 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-HF-7136         TCGA-HJ-7597         TCGA-IN-7806 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-IN-7808         TCGA-IP-7968 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 

Clustering(61) Variable = 14q loss
D61V1, survival
                    sevent
clus2                  0   1
  14Q LOSS CNV        13   1
  14Q LOSS WILD-TYPE 111  18
      14Q LOSS CNV 14Q LOSS WILD-TYPE 
                14                129 
      14Q LOSS CNV 14Q LOSS WILD-TYPE 
                 1                 18 
$`14Q LOSS CNV`
TCGA-BR-6458 TCGA-BR-7715 TCGA-BR-7959 TCGA-BR-8286 TCGA-BR-A4J1 TCGA-BR-A4J6 
        1.35         1.05         1.08         0.43         0.72         0.13 
TCGA-BR-A4PF TCGA-CG-4438 TCGA-CG-4477 TCGA-D7-6519 TCGA-D7-6520 TCGA-EQ-8122 
        0.72        54.05         1.02        15.65         9.63         7.79 
TCGA-FP-8631 TCGA-IN-7806 
        0.56         6.87 

$`14Q LOSS WILD-TYPE`
TCGA-B7-5816 TCGA-B7-5818 TCGA-BR-6452 TCGA-BR-6455 TCGA-BR-6457 TCGA-BR-6563 
        5.62         0.10         0.95         1.41         1.35         0.85 
TCGA-BR-6564 TCGA-BR-6565 TCGA-BR-6566 TCGA-BR-6705 TCGA-BR-6706 TCGA-BR-6707 
        0.82         0.62         0.62         1.71         2.17         0.99 
TCGA-BR-6709 TCGA-BR-6710 TCGA-BR-6801 TCGA-BR-6802 TCGA-BR-6803 TCGA-BR-6852 
        1.22         0.66         1.12         0.76         0.66         0.26 
TCGA-BR-7196 TCGA-BR-7197 TCGA-BR-7703 TCGA-BR-7704 TCGA-BR-7707 TCGA-BR-7716 
        1.22         1.48         0.46         1.25         0.13         0.82 
TCGA-BR-7717 TCGA-BR-7722 TCGA-BR-7723 TCGA-BR-7851 TCGA-BR-7901 TCGA-BR-7957 
        0.69         0.16         4.54         0.99         0.95         0.69 
TCGA-BR-7958 TCGA-BR-8059 TCGA-BR-8060 TCGA-BR-8077 TCGA-BR-8078 TCGA-BR-8080 
        0.16         0.82         1.32         0.69         0.95         0.49 
TCGA-BR-8081 TCGA-BR-8284 TCGA-BR-8285 TCGA-BR-8289 TCGA-BR-8291 TCGA-BR-8295 
        0.46         0.72         0.26         0.26         1.18         1.55 
TCGA-BR-8296 TCGA-BR-8297 TCGA-BR-8592 TCGA-BR-A4IU TCGA-BR-A4IV TCGA-BR-A4IY 
        1.48         0.76         0.20         0.59         0.92         0.39 
TCGA-BR-A4IZ TCGA-BR-A4J2 TCGA-BR-A4J4 TCGA-BR-A4J5 TCGA-BR-A4J8 TCGA-BR-A4J9 
        0.79         0.79         0.53         0.43         0.23         0.10 
TCGA-BR-A4QI TCGA-BR-A4QL TCGA-CD-5798 TCGA-CD-5799 TCGA-CD-5800 TCGA-CD-5801 
        0.49         2.24         0.82         0.69         0.36         0.49 
TCGA-CD-5802 TCGA-CD-5803 TCGA-CG-4300 TCGA-CG-4301 TCGA-CG-4304 TCGA-CG-4305 
        0.30         0.07        20.02         3.02        27.02        15.95 
TCGA-CG-4306 TCGA-CG-4436 TCGA-CG-4437 TCGA-CG-4440 TCGA-CG-4441 TCGA-CG-4443 
        1.02        52.96         8.05         4.01        14.01        29.98 
TCGA-CG-4444 TCGA-CG-4449 TCGA-CG-4455 TCGA-CG-4460 TCGA-CG-4462 TCGA-CG-4465 
       47.05        19.07        12.03        21.99         1.02         8.98 
TCGA-CG-4466 TCGA-CG-4469 TCGA-CG-4472 TCGA-CG-4474 TCGA-CG-5716 TCGA-CG-5717 
       18.94         7.07        12.00         1.02         1.02         6.94 
TCGA-CG-5718 TCGA-CG-5719 TCGA-CG-5720 TCGA-CG-5721 TCGA-CG-5722 TCGA-CG-5723 
        1.02         1.02         0.99         5.98         0.95        70.06 
TCGA-CG-5724 TCGA-CG-5725 TCGA-CG-5726 TCGA-CG-5727 TCGA-CG-5728 TCGA-CG-5730 
       12.03        15.02        28.96        31.04        65.10         4.01 
TCGA-CG-5732 TCGA-CG-5733 TCGA-CG-5734 TCGA-D7-5577 TCGA-D7-5578 TCGA-D7-5579 
       55.04        21.07         7.99         8.65         3.58         4.54 
TCGA-D7-6518 TCGA-D7-6521 TCGA-D7-6522 TCGA-D7-6524 TCGA-D7-6525 TCGA-D7-6526 
        9.80         8.19         6.90         0.69         5.95         6.61 
TCGA-D7-6527 TCGA-D7-6528 TCGA-D7-6815 TCGA-D7-6817 TCGA-D7-6818 TCGA-D7-6820 
        4.14         1.68         3.65         4.70         4.04         2.93 
TCGA-D7-6822 TCGA-EQ-5647 TCGA-F1-6177 TCGA-F1-6874 TCGA-F1-6875 TCGA-FP-7735 
        4.27         0.62         6.54         2.01        72.23         0.39 
TCGA-FP-7829 TCGA-FP-7916 TCGA-FP-7998 TCGA-FP-8099 TCGA-FP-8209 TCGA-FP-8210 
        0.20         3.02         3.58         1.02        59.05         5.03 
TCGA-HJ-7597 TCGA-IN-7808 TCGA-IP-7968 
       26.43         3.55         2.53 

      14Q LOSS CNV 14Q LOSS WILD-TYPE 
              0.13               0.07 
      14Q LOSS CNV 14Q LOSS WILD-TYPE 
             54.05              72.23 
      14Q LOSS CNV 14Q LOSS WILD-TYPE 
             1.065              1.320 
[1] "0.1 - 54.0 (1.1)" "0.1 - 72.2 (1.3)"
        TCGA-B7-5816         TCGA-B7-5818         TCGA-BR-6452 
"14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" 
        TCGA-BR-6455         TCGA-BR-6457         TCGA-BR-6458 
"14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE"       "14Q LOSS CNV" 
        TCGA-BR-6563         TCGA-BR-6564         TCGA-BR-6565 
"14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" 
        TCGA-BR-6566         TCGA-BR-6705         TCGA-BR-6706 
"14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" 
        TCGA-BR-6707         TCGA-BR-6709         TCGA-BR-6710 
"14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" 
        TCGA-BR-6801         TCGA-BR-6802         TCGA-BR-6803 
"14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" 
        TCGA-BR-6852         TCGA-BR-7196         TCGA-BR-7197 
"14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" 
        TCGA-BR-7703         TCGA-BR-7704         TCGA-BR-7707 
"14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" 
        TCGA-BR-7715         TCGA-BR-7716         TCGA-BR-7717 
      "14Q LOSS CNV" "14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" 
        TCGA-BR-7722         TCGA-BR-7723         TCGA-BR-7851 
"14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" 
        TCGA-BR-7901         TCGA-BR-7957         TCGA-BR-7958 
"14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" 
        TCGA-BR-7959         TCGA-BR-8059         TCGA-BR-8060 
      "14Q LOSS CNV" "14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" 
        TCGA-BR-8077         TCGA-BR-8078         TCGA-BR-8080 
"14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" 
        TCGA-BR-8081         TCGA-BR-8284         TCGA-BR-8285 
"14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" 
        TCGA-BR-8286         TCGA-BR-8289         TCGA-BR-8291 
      "14Q LOSS CNV" "14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" 
        TCGA-BR-8295         TCGA-BR-8296         TCGA-BR-8297 
"14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" 
        TCGA-BR-8592         TCGA-BR-A4IU         TCGA-BR-A4IV 
"14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" 
        TCGA-BR-A4IY         TCGA-BR-A4IZ         TCGA-BR-A4J1 
"14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE"       "14Q LOSS CNV" 
        TCGA-BR-A4J2         TCGA-BR-A4J4         TCGA-BR-A4J5 
"14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" 
        TCGA-BR-A4J6         TCGA-BR-A4J8         TCGA-BR-A4J9 
      "14Q LOSS CNV" "14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" 
        TCGA-BR-A4PF         TCGA-BR-A4QI         TCGA-BR-A4QL 
      "14Q LOSS CNV" "14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" 
        TCGA-CD-5798         TCGA-CD-5799         TCGA-CD-5800 
"14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" 
        TCGA-CD-5801         TCGA-CD-5802         TCGA-CD-5803 
"14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" 
        TCGA-CG-4300         TCGA-CG-4301         TCGA-CG-4304 
"14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" 
        TCGA-CG-4305         TCGA-CG-4306         TCGA-CG-4436 
"14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" 
        TCGA-CG-4437         TCGA-CG-4438         TCGA-CG-4440 
"14Q LOSS WILD-TYPE"       "14Q LOSS CNV" "14Q LOSS WILD-TYPE" 
        TCGA-CG-4441         TCGA-CG-4443         TCGA-CG-4444 
"14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" 
        TCGA-CG-4449         TCGA-CG-4455         TCGA-CG-4460 
"14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" 
        TCGA-CG-4462         TCGA-CG-4465         TCGA-CG-4466 
"14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" 
        TCGA-CG-4469         TCGA-CG-4472         TCGA-CG-4474 
"14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" 
        TCGA-CG-4477         TCGA-CG-5716         TCGA-CG-5717 
      "14Q LOSS CNV" "14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" 
        TCGA-CG-5718         TCGA-CG-5719         TCGA-CG-5720 
"14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" 
        TCGA-CG-5721         TCGA-CG-5722         TCGA-CG-5723 
"14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" 
        TCGA-CG-5724         TCGA-CG-5725         TCGA-CG-5726 
"14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" 
        TCGA-CG-5727         TCGA-CG-5728         TCGA-CG-5730 
"14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" 
        TCGA-CG-5732         TCGA-CG-5733         TCGA-CG-5734 
"14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" 
        TCGA-D7-5577         TCGA-D7-5578         TCGA-D7-5579 
"14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" 
        TCGA-D7-6518         TCGA-D7-6519         TCGA-D7-6520 
"14Q LOSS WILD-TYPE"       "14Q LOSS CNV"       "14Q LOSS CNV" 
        TCGA-D7-6521         TCGA-D7-6522         TCGA-D7-6524 
"14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" 
        TCGA-D7-6525         TCGA-D7-6526         TCGA-D7-6527 
"14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" 
        TCGA-D7-6528         TCGA-D7-6815         TCGA-D7-6817 
"14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" 
        TCGA-D7-6818         TCGA-D7-6820         TCGA-D7-6822 
"14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" 
        TCGA-EQ-5647         TCGA-EQ-8122         TCGA-F1-6177 
"14Q LOSS WILD-TYPE"       "14Q LOSS CNV" "14Q LOSS WILD-TYPE" 
        TCGA-F1-6874         TCGA-F1-6875         TCGA-FP-7735 
"14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" 
        TCGA-FP-7829         TCGA-FP-7916         TCGA-FP-7998 
"14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" 
        TCGA-FP-8099         TCGA-FP-8209         TCGA-FP-8210 
"14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" 
        TCGA-FP-8631         TCGA-HJ-7597         TCGA-IN-7806 
      "14Q LOSS CNV" "14Q LOSS WILD-TYPE"       "14Q LOSS CNV" 
        TCGA-IN-7808         TCGA-IP-7968 
"14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" 
        TCGA-B7-5816         TCGA-B7-5818         TCGA-BR-6452 
"14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" 
        TCGA-BR-6455         TCGA-BR-6457         TCGA-BR-6458 
"14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE"       "14Q LOSS CNV" 
        TCGA-BR-6563         TCGA-BR-6564         TCGA-BR-6565 
"14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" 
        TCGA-BR-6566         TCGA-BR-6705         TCGA-BR-6706 
"14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" 
        TCGA-BR-6707         TCGA-BR-6709         TCGA-BR-6710 
"14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" 
        TCGA-BR-6801         TCGA-BR-6802         TCGA-BR-6803 
"14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" 
        TCGA-BR-6852         TCGA-BR-7196         TCGA-BR-7197 
"14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" 
        TCGA-BR-7703         TCGA-BR-7704         TCGA-BR-7707 
"14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" 
        TCGA-BR-7715         TCGA-BR-7716         TCGA-BR-7717 
      "14Q LOSS CNV" "14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" 
        TCGA-BR-7722         TCGA-BR-7723         TCGA-BR-7851 
"14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" 
        TCGA-BR-7901         TCGA-BR-7957         TCGA-BR-7958 
"14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" 
        TCGA-BR-7959         TCGA-BR-8059         TCGA-BR-8060 
      "14Q LOSS CNV" "14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" 
        TCGA-BR-8077         TCGA-BR-8078         TCGA-BR-8080 
"14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" 
        TCGA-BR-8081         TCGA-BR-8284         TCGA-BR-8285 
"14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" 
        TCGA-BR-8286         TCGA-BR-8289         TCGA-BR-8291 
      "14Q LOSS CNV" "14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" 
        TCGA-BR-8295         TCGA-BR-8296         TCGA-BR-8297 
"14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" 
        TCGA-BR-8592         TCGA-BR-A4IU         TCGA-BR-A4IV 
"14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" 
        TCGA-BR-A4IY         TCGA-BR-A4IZ         TCGA-BR-A4J1 
"14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE"       "14Q LOSS CNV" 
        TCGA-BR-A4J2         TCGA-BR-A4J4         TCGA-BR-A4J5 
"14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" 
        TCGA-BR-A4J6         TCGA-BR-A4J8         TCGA-BR-A4J9 
      "14Q LOSS CNV" "14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" 
        TCGA-BR-A4PF         TCGA-BR-A4QI         TCGA-BR-A4QL 
      "14Q LOSS CNV" "14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" 
        TCGA-CD-5798         TCGA-CD-5799         TCGA-CD-5800 
"14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" 
        TCGA-CD-5801         TCGA-CD-5802         TCGA-CD-5803 
"14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" 
        TCGA-CG-4300         TCGA-CG-4301         TCGA-CG-4304 
"14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" 
        TCGA-CG-4305         TCGA-CG-4306         TCGA-CG-4436 
"14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" 
        TCGA-CG-4437         TCGA-CG-4438         TCGA-CG-4440 
"14Q LOSS WILD-TYPE"       "14Q LOSS CNV" "14Q LOSS WILD-TYPE" 
        TCGA-CG-4441         TCGA-CG-4443         TCGA-CG-4444 
"14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" 
        TCGA-CG-4449         TCGA-CG-4455         TCGA-CG-4460 
"14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" 
        TCGA-CG-4462         TCGA-CG-4465         TCGA-CG-4466 
"14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" 
        TCGA-CG-4469         TCGA-CG-4472         TCGA-CG-4474 
"14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" 
        TCGA-CG-4477         TCGA-CG-5716         TCGA-CG-5717 
      "14Q LOSS CNV" "14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" 
        TCGA-CG-5718         TCGA-CG-5719         TCGA-CG-5720 
"14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" 
        TCGA-CG-5721         TCGA-CG-5722         TCGA-CG-5723 
"14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" 
        TCGA-CG-5724         TCGA-CG-5725         TCGA-CG-5726 
"14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" 
        TCGA-CG-5727         TCGA-CG-5728         TCGA-CG-5730 
"14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" 
        TCGA-CG-5732         TCGA-CG-5733         TCGA-CG-5734 
"14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" 
        TCGA-D7-5577         TCGA-D7-5578         TCGA-D7-5579 
"14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" 
        TCGA-D7-6518         TCGA-D7-6519         TCGA-D7-6520 
"14Q LOSS WILD-TYPE"       "14Q LOSS CNV"       "14Q LOSS CNV" 
        TCGA-D7-6521         TCGA-D7-6522         TCGA-D7-6524 
"14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" 
        TCGA-D7-6525         TCGA-D7-6526         TCGA-D7-6527 
"14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" 
        TCGA-D7-6528         TCGA-D7-6815         TCGA-D7-6817 
"14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" 
        TCGA-D7-6818         TCGA-D7-6820         TCGA-D7-6822 
"14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" 
        TCGA-EQ-5647         TCGA-EQ-8122         TCGA-F1-6177 
"14Q LOSS WILD-TYPE"       "14Q LOSS CNV" "14Q LOSS WILD-TYPE" 
        TCGA-F1-6874         TCGA-F1-6875         TCGA-FP-7735 
"14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" 
        TCGA-FP-7829         TCGA-FP-7916         TCGA-FP-7998 
"14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" 
        TCGA-FP-8099         TCGA-FP-8209         TCGA-FP-8210 
"14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" 
        TCGA-FP-8631         TCGA-HJ-7597         TCGA-IN-7806 
      "14Q LOSS CNV" "14Q LOSS WILD-TYPE"       "14Q LOSS CNV" 
        TCGA-IN-7808         TCGA-IP-7968 
"14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" 
        TCGA-B7-5816         TCGA-B7-5818         TCGA-BR-6452 
"14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" 
        TCGA-BR-6455         TCGA-BR-6457         TCGA-BR-6458 
"14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE"       "14Q LOSS CNV" 
        TCGA-BR-6563         TCGA-BR-6564         TCGA-BR-6565 
"14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" 
        TCGA-BR-6566         TCGA-BR-6705         TCGA-BR-6706 
"14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" 
        TCGA-BR-6707         TCGA-BR-6709         TCGA-BR-6710 
"14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" 
        TCGA-BR-6801         TCGA-BR-6802         TCGA-BR-6803 
"14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" 
        TCGA-BR-6852         TCGA-BR-7196         TCGA-BR-7197 
"14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" 
        TCGA-BR-7703         TCGA-BR-7704         TCGA-BR-7707 
"14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" 
        TCGA-BR-7715         TCGA-BR-7716         TCGA-BR-7717 
      "14Q LOSS CNV" "14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" 
        TCGA-BR-7722         TCGA-BR-7723         TCGA-BR-7851 
"14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" 
        TCGA-BR-7901         TCGA-BR-7957         TCGA-BR-7958 
"14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" 
        TCGA-BR-7959         TCGA-BR-8059         TCGA-BR-8060 
      "14Q LOSS CNV" "14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" 
        TCGA-BR-8077         TCGA-BR-8078         TCGA-BR-8080 
"14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" 
        TCGA-BR-8081         TCGA-BR-8284         TCGA-BR-8285 
"14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" 
        TCGA-BR-8286         TCGA-BR-8289         TCGA-BR-8291 
      "14Q LOSS CNV" "14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" 
        TCGA-BR-8295         TCGA-BR-8296         TCGA-BR-8297 
"14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" 
        TCGA-BR-8592         TCGA-BR-A4IU         TCGA-BR-A4IV 
"14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" 
        TCGA-BR-A4IY         TCGA-BR-A4IZ         TCGA-BR-A4J1 
"14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE"       "14Q LOSS CNV" 
        TCGA-BR-A4J2         TCGA-BR-A4J4         TCGA-BR-A4J5 
"14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" 
        TCGA-BR-A4J6         TCGA-BR-A4J8         TCGA-BR-A4J9 
      "14Q LOSS CNV" "14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" 
        TCGA-BR-A4PF         TCGA-BR-A4QI         TCGA-BR-A4QL 
      "14Q LOSS CNV" "14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" 
        TCGA-CD-5798         TCGA-CD-5799         TCGA-CD-5800 
"14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" 
        TCGA-CD-5801         TCGA-CD-5802         TCGA-CD-5803 
"14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" 
        TCGA-CG-4300         TCGA-CG-4301         TCGA-CG-4304 
"14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" 
        TCGA-CG-4305         TCGA-CG-4306         TCGA-CG-4436 
"14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" 
        TCGA-CG-4437         TCGA-CG-4438         TCGA-CG-4440 
"14Q LOSS WILD-TYPE"       "14Q LOSS CNV" "14Q LOSS WILD-TYPE" 
        TCGA-CG-4441         TCGA-CG-4443         TCGA-CG-4444 
"14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" 
        TCGA-CG-4449         TCGA-CG-4455         TCGA-CG-4460 
"14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" 
        TCGA-CG-4462         TCGA-CG-4465         TCGA-CG-4466 
"14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" 
        TCGA-CG-4469         TCGA-CG-4472         TCGA-CG-4474 
"14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" 
        TCGA-CG-4477         TCGA-CG-5716         TCGA-CG-5717 
      "14Q LOSS CNV" "14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" 
        TCGA-CG-5718         TCGA-CG-5719         TCGA-CG-5720 
"14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" 
        TCGA-CG-5721         TCGA-CG-5722         TCGA-CG-5723 
"14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" 
        TCGA-CG-5724         TCGA-CG-5725         TCGA-CG-5726 
"14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" 
        TCGA-CG-5727         TCGA-CG-5728         TCGA-CG-5730 
"14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" 
        TCGA-CG-5732         TCGA-CG-5733         TCGA-CG-5734 
"14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" 
        TCGA-D7-5577         TCGA-D7-5578         TCGA-D7-5579 
"14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" 
        TCGA-D7-6518         TCGA-D7-6519         TCGA-D7-6520 
"14Q LOSS WILD-TYPE"       "14Q LOSS CNV"       "14Q LOSS CNV" 
        TCGA-D7-6521         TCGA-D7-6522         TCGA-D7-6524 
"14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" 
        TCGA-D7-6525         TCGA-D7-6526         TCGA-D7-6527 
"14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" 
        TCGA-D7-6528         TCGA-D7-6815         TCGA-D7-6817 
"14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" 
        TCGA-D7-6818         TCGA-D7-6820         TCGA-D7-6822 
"14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" 
        TCGA-EQ-5647         TCGA-EQ-8122         TCGA-F1-6177 
"14Q LOSS WILD-TYPE"       "14Q LOSS CNV" "14Q LOSS WILD-TYPE" 
        TCGA-F1-6874         TCGA-F1-6875         TCGA-FP-7735 
"14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" 
        TCGA-FP-7829         TCGA-FP-7916         TCGA-FP-7998 
"14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" 
        TCGA-FP-8099         TCGA-FP-8209         TCGA-FP-8210 
"14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" 
        TCGA-FP-8631         TCGA-HJ-7597         TCGA-IN-7806 
      "14Q LOSS CNV" "14Q LOSS WILD-TYPE"       "14Q LOSS CNV" 
        TCGA-IN-7808         TCGA-IP-7968 
"14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" 
[1] "hr=" "1.7"
D61V2, continuous
D61V3, binary
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  14Q LOSS CNV          5   11
  14Q LOSS WILD-TYPE   67   97
        clus
vv       14Q LOSS CNV 14Q LOSS WILD-TYPE
  FEMALE            5                 67
  MALE             11                 97
                    vv
clus                 STOMACH  ADENOCARCINOMA  DIFFUSE TYPE
  14Q LOSS CNV                                           0
  14Q LOSS WILD-TYPE                                    10
                    vv
clus                 STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  14Q LOSS CNV                                                            4
  14Q LOSS WILD-TYPE                                                     12
                    vv
clus                 STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  14Q LOSS CNV                                                                       2
  14Q LOSS WILD-TYPE                                                                 6
                    vv
clus                 STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE
  14Q LOSS CNV                                                              1
  14Q LOSS WILD-TYPE                                                        2
                    vv
clus                 STOMACH ADENOCARCINOMA  SIGNET RING TYPE
  14Q LOSS CNV                                              0
  14Q LOSS WILD-TYPE                                        1
                    vv
clus                 STOMACH ADENOCARCINOMA - DIFFUSE TYPE
  14Q LOSS CNV                                           2
  14Q LOSS WILD-TYPE                                    14
                    vv
clus                 STOMACH ADENOCARCINOMA - NOT OTHERWISE SPECIFIED (NOS)
  14Q LOSS CNV                                                            4
  14Q LOSS WILD-TYPE                                                     69
                    vv
clus                 STOMACH INTESTINAL ADENOCARCINOMA - MUCINOUS TYPE
  14Q LOSS CNV                                                       0
  14Q LOSS WILD-TYPE                                                 7
                    vv
clus                 STOMACH INTESTINAL ADENOCARCINOMA - PAPILLARY TYPE
  14Q LOSS CNV                                                        0
  14Q LOSS WILD-TYPE                                                  3
                    vv
clus                 STOMACH INTESTINAL ADENOCARCINOMA - TUBULAR TYPE
  14Q LOSS CNV                                                      1
  14Q LOSS WILD-TYPE                                                9
                    vv
clus                 STOMACH INTESTINAL ADENOCARCINOMA - TYPE NOT OTHERWISE SPECIFIED (NOS)
  14Q LOSS CNV                                                                            2
  14Q LOSS WILD-TYPE                                                                     26
D61V4, multiclass
                    vv
clus                 T1 T2 T3 T4
  14Q LOSS CNV        0  4  3  1
  14Q LOSS WILD-TYPE  6 48 53 17
D61V5, multiclass
    clus
vv   14Q LOSS CNV 14Q LOSS WILD-TYPE
  T1            0                  6
  T2            4                 48
  T3            3                 53
  T4            1                 17
                    vv
clus                 N0 N1 N2 N3
  14Q LOSS CNV        2  4  2  0
  14Q LOSS WILD-TYPE 42 45 21 15
D61V6, multiclass
    clus
vv   14Q LOSS CNV 14Q LOSS WILD-TYPE
  N0            2                 42
  N1            4                 45
  N2            2                 21
  N3            0                 15
                    vv
clus                  M0  M1  MX
  14Q LOSS CNV         9   0   0
  14Q LOSS WILD-TYPE 109  16   8
D61V7, multiclass
    clus
vv   14Q LOSS CNV 14Q LOSS WILD-TYPE
  M0            9                109
  M1            0                 16
  MX            0                  8
                    vv
clus                  I II III IV
  14Q LOSS CNV        1  3   3  1
  14Q LOSS WILD-TYPE 23 34  36 25
D61V8, multiclass
     clus
vv    14Q LOSS CNV 14Q LOSS WILD-TYPE
  I              1                 23
  II             3                 34
  III            3                 36
  IV             1                 25
D61V9, binary
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  14Q LOSS CNV          0   16
  14Q LOSS WILD-TYPE    5  159
     clus
vv    14Q LOSS CNV 14Q LOSS WILD-TYPE
  NO             0                  5
  YES           16                159
                    vv
clus                  R0  R1  R2  RX
  14Q LOSS CNV        13   0   0   2
  14Q LOSS WILD-TYPE 112   7  12  23
D61V10, multiclass
    clus
vv   14Q LOSS CNV 14Q LOSS WILD-TYPE
  R0           13                112
  R1            0                  7
  R2            0                 12
  RX            2                 23
D61V11, continuous

Clustering(62) Variable = 15q loss
D62V1, survival
                    sevent
clus2                  0   1
  15Q LOSS CNV        11   2
  15Q LOSS WILD-TYPE 113  17
      15Q LOSS CNV 15Q LOSS WILD-TYPE 
                13                130 
      15Q LOSS CNV 15Q LOSS WILD-TYPE 
                 2                 17 
$`15Q LOSS CNV`
TCGA-BR-7704 TCGA-BR-8286 TCGA-BR-8289 TCGA-BR-A4J1 TCGA-BR-A4QI TCGA-CG-4436 
        1.25         0.43         0.26         0.72         0.49        52.96 
TCGA-CG-4466 TCGA-CG-5724 TCGA-D7-6519 TCGA-D7-6527 TCGA-D7-6528 TCGA-D7-6817 
       18.94        12.03        15.65         4.14         1.68         4.70 
TCGA-EQ-8122 
        7.79 

$`15Q LOSS WILD-TYPE`
TCGA-B7-5816 TCGA-B7-5818 TCGA-BR-6452 TCGA-BR-6455 TCGA-BR-6457 TCGA-BR-6458 
        5.62         0.10         0.95         1.41         1.35         1.35 
TCGA-BR-6563 TCGA-BR-6564 TCGA-BR-6565 TCGA-BR-6566 TCGA-BR-6705 TCGA-BR-6706 
        0.85         0.82         0.62         0.62         1.71         2.17 
TCGA-BR-6707 TCGA-BR-6709 TCGA-BR-6710 TCGA-BR-6801 TCGA-BR-6802 TCGA-BR-6803 
        0.99         1.22         0.66         1.12         0.76         0.66 
TCGA-BR-6852 TCGA-BR-7196 TCGA-BR-7197 TCGA-BR-7703 TCGA-BR-7707 TCGA-BR-7715 
        0.26         1.22         1.48         0.46         0.13         1.05 
TCGA-BR-7716 TCGA-BR-7717 TCGA-BR-7722 TCGA-BR-7723 TCGA-BR-7851 TCGA-BR-7901 
        0.82         0.69         0.16         4.54         0.99         0.95 
TCGA-BR-7957 TCGA-BR-7958 TCGA-BR-7959 TCGA-BR-8059 TCGA-BR-8060 TCGA-BR-8077 
        0.69         0.16         1.08         0.82         1.32         0.69 
TCGA-BR-8078 TCGA-BR-8080 TCGA-BR-8081 TCGA-BR-8284 TCGA-BR-8285 TCGA-BR-8291 
        0.95         0.49         0.46         0.72         0.26         1.18 
TCGA-BR-8295 TCGA-BR-8296 TCGA-BR-8297 TCGA-BR-8592 TCGA-BR-A4IU TCGA-BR-A4IV 
        1.55         1.48         0.76         0.20         0.59         0.92 
TCGA-BR-A4IY TCGA-BR-A4IZ TCGA-BR-A4J2 TCGA-BR-A4J4 TCGA-BR-A4J5 TCGA-BR-A4J6 
        0.39         0.79         0.79         0.53         0.43         0.13 
TCGA-BR-A4J8 TCGA-BR-A4J9 TCGA-BR-A4PF TCGA-BR-A4QL TCGA-CD-5798 TCGA-CD-5799 
        0.23         0.10         0.72         2.24         0.82         0.69 
TCGA-CD-5800 TCGA-CD-5801 TCGA-CD-5802 TCGA-CD-5803 TCGA-CG-4300 TCGA-CG-4301 
        0.36         0.49         0.30         0.07        20.02         3.02 
TCGA-CG-4304 TCGA-CG-4305 TCGA-CG-4306 TCGA-CG-4437 TCGA-CG-4438 TCGA-CG-4440 
       27.02        15.95         1.02         8.05        54.05         4.01 
TCGA-CG-4441 TCGA-CG-4443 TCGA-CG-4444 TCGA-CG-4449 TCGA-CG-4455 TCGA-CG-4460 
       14.01        29.98        47.05        19.07        12.03        21.99 
TCGA-CG-4462 TCGA-CG-4465 TCGA-CG-4469 TCGA-CG-4472 TCGA-CG-4474 TCGA-CG-4477 
        1.02         8.98         7.07        12.00         1.02         1.02 
TCGA-CG-5716 TCGA-CG-5717 TCGA-CG-5718 TCGA-CG-5719 TCGA-CG-5720 TCGA-CG-5721 
        1.02         6.94         1.02         1.02         0.99         5.98 
TCGA-CG-5722 TCGA-CG-5723 TCGA-CG-5725 TCGA-CG-5726 TCGA-CG-5727 TCGA-CG-5728 
        0.95        70.06        15.02        28.96        31.04        65.10 
TCGA-CG-5730 TCGA-CG-5732 TCGA-CG-5733 TCGA-CG-5734 TCGA-D7-5577 TCGA-D7-5578 
        4.01        55.04        21.07         7.99         8.65         3.58 
TCGA-D7-5579 TCGA-D7-6518 TCGA-D7-6520 TCGA-D7-6521 TCGA-D7-6522 TCGA-D7-6524 
        4.54         9.80         9.63         8.19         6.90         0.69 
TCGA-D7-6525 TCGA-D7-6526 TCGA-D7-6815 TCGA-D7-6818 TCGA-D7-6820 TCGA-D7-6822 
        5.95         6.61         3.65         4.04         2.93         4.27 
TCGA-EQ-5647 TCGA-F1-6177 TCGA-F1-6874 TCGA-F1-6875 TCGA-FP-7735 TCGA-FP-7829 
        0.62         6.54         2.01        72.23         0.39         0.20 
TCGA-FP-7916 TCGA-FP-7998 TCGA-FP-8099 TCGA-FP-8209 TCGA-FP-8210 TCGA-FP-8631 
        3.02         3.58         1.02        59.05         5.03         0.56 
TCGA-HJ-7597 TCGA-IN-7806 TCGA-IN-7808 TCGA-IP-7968 
       26.43         6.87         3.55         2.53 

      15Q LOSS CNV 15Q LOSS WILD-TYPE 
              0.26               0.07 
      15Q LOSS CNV 15Q LOSS WILD-TYPE 
             52.96              72.23 
      15Q LOSS CNV 15Q LOSS WILD-TYPE 
              4.14               1.20 
[1] "0.3 - 53.0 (4.1)" "0.1 - 72.2 (1.2)"
        TCGA-B7-5816         TCGA-B7-5818         TCGA-BR-6452 
"15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" 
        TCGA-BR-6455         TCGA-BR-6457         TCGA-BR-6458 
"15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" 
        TCGA-BR-6563         TCGA-BR-6564         TCGA-BR-6565 
"15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" 
        TCGA-BR-6566         TCGA-BR-6705         TCGA-BR-6706 
"15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" 
        TCGA-BR-6707         TCGA-BR-6709         TCGA-BR-6710 
"15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" 
        TCGA-BR-6801         TCGA-BR-6802         TCGA-BR-6803 
"15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" 
        TCGA-BR-6852         TCGA-BR-7196         TCGA-BR-7197 
"15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" 
        TCGA-BR-7703         TCGA-BR-7704         TCGA-BR-7707 
"15Q LOSS WILD-TYPE"       "15Q LOSS CNV" "15Q LOSS WILD-TYPE" 
        TCGA-BR-7715         TCGA-BR-7716         TCGA-BR-7717 
"15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" 
        TCGA-BR-7722         TCGA-BR-7723         TCGA-BR-7851 
"15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" 
        TCGA-BR-7901         TCGA-BR-7957         TCGA-BR-7958 
"15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" 
        TCGA-BR-7959         TCGA-BR-8059         TCGA-BR-8060 
"15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" 
        TCGA-BR-8077         TCGA-BR-8078         TCGA-BR-8080 
"15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" 
        TCGA-BR-8081         TCGA-BR-8284         TCGA-BR-8285 
"15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" 
        TCGA-BR-8286         TCGA-BR-8289         TCGA-BR-8291 
      "15Q LOSS CNV"       "15Q LOSS CNV" "15Q LOSS WILD-TYPE" 
        TCGA-BR-8295         TCGA-BR-8296         TCGA-BR-8297 
"15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" 
        TCGA-BR-8592         TCGA-BR-A4IU         TCGA-BR-A4IV 
"15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" 
        TCGA-BR-A4IY         TCGA-BR-A4IZ         TCGA-BR-A4J1 
"15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE"       "15Q LOSS CNV" 
        TCGA-BR-A4J2         TCGA-BR-A4J4         TCGA-BR-A4J5 
"15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" 
        TCGA-BR-A4J6         TCGA-BR-A4J8         TCGA-BR-A4J9 
"15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" 
        TCGA-BR-A4PF         TCGA-BR-A4QI         TCGA-BR-A4QL 
"15Q LOSS WILD-TYPE"       "15Q LOSS CNV" "15Q LOSS WILD-TYPE" 
        TCGA-CD-5798         TCGA-CD-5799         TCGA-CD-5800 
"15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" 
        TCGA-CD-5801         TCGA-CD-5802         TCGA-CD-5803 
"15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" 
        TCGA-CG-4300         TCGA-CG-4301         TCGA-CG-4304 
"15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" 
        TCGA-CG-4305         TCGA-CG-4306         TCGA-CG-4436 
"15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE"       "15Q LOSS CNV" 
        TCGA-CG-4437         TCGA-CG-4438         TCGA-CG-4440 
"15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" 
        TCGA-CG-4441         TCGA-CG-4443         TCGA-CG-4444 
"15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" 
        TCGA-CG-4449         TCGA-CG-4455         TCGA-CG-4460 
"15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" 
        TCGA-CG-4462         TCGA-CG-4465         TCGA-CG-4466 
"15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE"       "15Q LOSS CNV" 
        TCGA-CG-4469         TCGA-CG-4472         TCGA-CG-4474 
"15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" 
        TCGA-CG-4477         TCGA-CG-5716         TCGA-CG-5717 
"15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" 
        TCGA-CG-5718         TCGA-CG-5719         TCGA-CG-5720 
"15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" 
        TCGA-CG-5721         TCGA-CG-5722         TCGA-CG-5723 
"15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" 
        TCGA-CG-5724         TCGA-CG-5725         TCGA-CG-5726 
      "15Q LOSS CNV" "15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" 
        TCGA-CG-5727         TCGA-CG-5728         TCGA-CG-5730 
"15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" 
        TCGA-CG-5732         TCGA-CG-5733         TCGA-CG-5734 
"15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" 
        TCGA-D7-5577         TCGA-D7-5578         TCGA-D7-5579 
"15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" 
        TCGA-D7-6518         TCGA-D7-6519         TCGA-D7-6520 
"15Q LOSS WILD-TYPE"       "15Q LOSS CNV" "15Q LOSS WILD-TYPE" 
        TCGA-D7-6521         TCGA-D7-6522         TCGA-D7-6524 
"15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" 
        TCGA-D7-6525         TCGA-D7-6526         TCGA-D7-6527 
"15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE"       "15Q LOSS CNV" 
        TCGA-D7-6528         TCGA-D7-6815         TCGA-D7-6817 
      "15Q LOSS CNV" "15Q LOSS WILD-TYPE"       "15Q LOSS CNV" 
        TCGA-D7-6818         TCGA-D7-6820         TCGA-D7-6822 
"15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" 
        TCGA-EQ-5647         TCGA-EQ-8122         TCGA-F1-6177 
"15Q LOSS WILD-TYPE"       "15Q LOSS CNV" "15Q LOSS WILD-TYPE" 
        TCGA-F1-6874         TCGA-F1-6875         TCGA-FP-7735 
"15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" 
        TCGA-FP-7829         TCGA-FP-7916         TCGA-FP-7998 
"15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" 
        TCGA-FP-8099         TCGA-FP-8209         TCGA-FP-8210 
"15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" 
        TCGA-FP-8631         TCGA-HJ-7597         TCGA-IN-7806 
"15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" 
        TCGA-IN-7808         TCGA-IP-7968 
"15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" 
        TCGA-B7-5816         TCGA-B7-5818         TCGA-BR-6452 
"15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" 
        TCGA-BR-6455         TCGA-BR-6457         TCGA-BR-6458 
"15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" 
        TCGA-BR-6563         TCGA-BR-6564         TCGA-BR-6565 
"15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" 
        TCGA-BR-6566         TCGA-BR-6705         TCGA-BR-6706 
"15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" 
        TCGA-BR-6707         TCGA-BR-6709         TCGA-BR-6710 
"15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" 
        TCGA-BR-6801         TCGA-BR-6802         TCGA-BR-6803 
"15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" 
        TCGA-BR-6852         TCGA-BR-7196         TCGA-BR-7197 
"15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" 
        TCGA-BR-7703         TCGA-BR-7704         TCGA-BR-7707 
"15Q LOSS WILD-TYPE"       "15Q LOSS CNV" "15Q LOSS WILD-TYPE" 
        TCGA-BR-7715         TCGA-BR-7716         TCGA-BR-7717 
"15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" 
        TCGA-BR-7722         TCGA-BR-7723         TCGA-BR-7851 
"15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" 
        TCGA-BR-7901         TCGA-BR-7957         TCGA-BR-7958 
"15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" 
        TCGA-BR-7959         TCGA-BR-8059         TCGA-BR-8060 
"15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" 
        TCGA-BR-8077         TCGA-BR-8078         TCGA-BR-8080 
"15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" 
        TCGA-BR-8081         TCGA-BR-8284         TCGA-BR-8285 
"15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" 
        TCGA-BR-8286         TCGA-BR-8289         TCGA-BR-8291 
      "15Q LOSS CNV"       "15Q LOSS CNV" "15Q LOSS WILD-TYPE" 
        TCGA-BR-8295         TCGA-BR-8296         TCGA-BR-8297 
"15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" 
        TCGA-BR-8592         TCGA-BR-A4IU         TCGA-BR-A4IV 
"15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" 
        TCGA-BR-A4IY         TCGA-BR-A4IZ         TCGA-BR-A4J1 
"15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE"       "15Q LOSS CNV" 
        TCGA-BR-A4J2         TCGA-BR-A4J4         TCGA-BR-A4J5 
"15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" 
        TCGA-BR-A4J6         TCGA-BR-A4J8         TCGA-BR-A4J9 
"15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" 
        TCGA-BR-A4PF         TCGA-BR-A4QI         TCGA-BR-A4QL 
"15Q LOSS WILD-TYPE"       "15Q LOSS CNV" "15Q LOSS WILD-TYPE" 
        TCGA-CD-5798         TCGA-CD-5799         TCGA-CD-5800 
"15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" 
        TCGA-CD-5801         TCGA-CD-5802         TCGA-CD-5803 
"15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" 
        TCGA-CG-4300         TCGA-CG-4301         TCGA-CG-4304 
"15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" 
        TCGA-CG-4305         TCGA-CG-4306         TCGA-CG-4436 
"15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE"       "15Q LOSS CNV" 
        TCGA-CG-4437         TCGA-CG-4438         TCGA-CG-4440 
"15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" 
        TCGA-CG-4441         TCGA-CG-4443         TCGA-CG-4444 
"15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" 
        TCGA-CG-4449         TCGA-CG-4455         TCGA-CG-4460 
"15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" 
        TCGA-CG-4462         TCGA-CG-4465         TCGA-CG-4466 
"15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE"       "15Q LOSS CNV" 
        TCGA-CG-4469         TCGA-CG-4472         TCGA-CG-4474 
"15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" 
        TCGA-CG-4477         TCGA-CG-5716         TCGA-CG-5717 
"15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" 
        TCGA-CG-5718         TCGA-CG-5719         TCGA-CG-5720 
"15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" 
        TCGA-CG-5721         TCGA-CG-5722         TCGA-CG-5723 
"15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" 
        TCGA-CG-5724         TCGA-CG-5725         TCGA-CG-5726 
      "15Q LOSS CNV" "15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" 
        TCGA-CG-5727         TCGA-CG-5728         TCGA-CG-5730 
"15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" 
        TCGA-CG-5732         TCGA-CG-5733         TCGA-CG-5734 
"15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" 
        TCGA-D7-5577         TCGA-D7-5578         TCGA-D7-5579 
"15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" 
        TCGA-D7-6518         TCGA-D7-6519         TCGA-D7-6520 
"15Q LOSS WILD-TYPE"       "15Q LOSS CNV" "15Q LOSS WILD-TYPE" 
        TCGA-D7-6521         TCGA-D7-6522         TCGA-D7-6524 
"15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" 
        TCGA-D7-6525         TCGA-D7-6526         TCGA-D7-6527 
"15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE"       "15Q LOSS CNV" 
        TCGA-D7-6528         TCGA-D7-6815         TCGA-D7-6817 
      "15Q LOSS CNV" "15Q LOSS WILD-TYPE"       "15Q LOSS CNV" 
        TCGA-D7-6818         TCGA-D7-6820         TCGA-D7-6822 
"15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" 
        TCGA-EQ-5647         TCGA-EQ-8122         TCGA-F1-6177 
"15Q LOSS WILD-TYPE"       "15Q LOSS CNV" "15Q LOSS WILD-TYPE" 
        TCGA-F1-6874         TCGA-F1-6875         TCGA-FP-7735 
"15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" 
        TCGA-FP-7829         TCGA-FP-7916         TCGA-FP-7998 
"15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" 
        TCGA-FP-8099         TCGA-FP-8209         TCGA-FP-8210 
"15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" 
        TCGA-FP-8631         TCGA-HJ-7597         TCGA-IN-7806 
"15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" 
        TCGA-IN-7808         TCGA-IP-7968 
"15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" 
        TCGA-B7-5816         TCGA-B7-5818         TCGA-BR-6452 
"15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" 
        TCGA-BR-6455         TCGA-BR-6457         TCGA-BR-6458 
"15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" 
        TCGA-BR-6563         TCGA-BR-6564         TCGA-BR-6565 
"15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" 
        TCGA-BR-6566         TCGA-BR-6705         TCGA-BR-6706 
"15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" 
        TCGA-BR-6707         TCGA-BR-6709         TCGA-BR-6710 
"15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" 
        TCGA-BR-6801         TCGA-BR-6802         TCGA-BR-6803 
"15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" 
        TCGA-BR-6852         TCGA-BR-7196         TCGA-BR-7197 
"15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" 
        TCGA-BR-7703         TCGA-BR-7704         TCGA-BR-7707 
"15Q LOSS WILD-TYPE"       "15Q LOSS CNV" "15Q LOSS WILD-TYPE" 
        TCGA-BR-7715         TCGA-BR-7716         TCGA-BR-7717 
"15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" 
        TCGA-BR-7722         TCGA-BR-7723         TCGA-BR-7851 
"15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" 
        TCGA-BR-7901         TCGA-BR-7957         TCGA-BR-7958 
"15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" 
        TCGA-BR-7959         TCGA-BR-8059         TCGA-BR-8060 
"15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" 
        TCGA-BR-8077         TCGA-BR-8078         TCGA-BR-8080 
"15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" 
        TCGA-BR-8081         TCGA-BR-8284         TCGA-BR-8285 
"15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" 
        TCGA-BR-8286         TCGA-BR-8289         TCGA-BR-8291 
      "15Q LOSS CNV"       "15Q LOSS CNV" "15Q LOSS WILD-TYPE" 
        TCGA-BR-8295         TCGA-BR-8296         TCGA-BR-8297 
"15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" 
        TCGA-BR-8592         TCGA-BR-A4IU         TCGA-BR-A4IV 
"15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" 
        TCGA-BR-A4IY         TCGA-BR-A4IZ         TCGA-BR-A4J1 
"15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE"       "15Q LOSS CNV" 
        TCGA-BR-A4J2         TCGA-BR-A4J4         TCGA-BR-A4J5 
"15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" 
        TCGA-BR-A4J6         TCGA-BR-A4J8         TCGA-BR-A4J9 
"15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" 
        TCGA-BR-A4PF         TCGA-BR-A4QI         TCGA-BR-A4QL 
"15Q LOSS WILD-TYPE"       "15Q LOSS CNV" "15Q LOSS WILD-TYPE" 
        TCGA-CD-5798         TCGA-CD-5799         TCGA-CD-5800 
"15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" 
        TCGA-CD-5801         TCGA-CD-5802         TCGA-CD-5803 
"15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" 
        TCGA-CG-4300         TCGA-CG-4301         TCGA-CG-4304 
"15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" 
        TCGA-CG-4305         TCGA-CG-4306         TCGA-CG-4436 
"15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE"       "15Q LOSS CNV" 
        TCGA-CG-4437         TCGA-CG-4438         TCGA-CG-4440 
"15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" 
        TCGA-CG-4441         TCGA-CG-4443         TCGA-CG-4444 
"15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" 
        TCGA-CG-4449         TCGA-CG-4455         TCGA-CG-4460 
"15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" 
        TCGA-CG-4462         TCGA-CG-4465         TCGA-CG-4466 
"15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE"       "15Q LOSS CNV" 
        TCGA-CG-4469         TCGA-CG-4472         TCGA-CG-4474 
"15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" 
        TCGA-CG-4477         TCGA-CG-5716         TCGA-CG-5717 
"15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" 
        TCGA-CG-5718         TCGA-CG-5719         TCGA-CG-5720 
"15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" 
        TCGA-CG-5721         TCGA-CG-5722         TCGA-CG-5723 
"15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" 
        TCGA-CG-5724         TCGA-CG-5725         TCGA-CG-5726 
      "15Q LOSS CNV" "15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" 
        TCGA-CG-5727         TCGA-CG-5728         TCGA-CG-5730 
"15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" 
        TCGA-CG-5732         TCGA-CG-5733         TCGA-CG-5734 
"15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" 
        TCGA-D7-5577         TCGA-D7-5578         TCGA-D7-5579 
"15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" 
        TCGA-D7-6518         TCGA-D7-6519         TCGA-D7-6520 
"15Q LOSS WILD-TYPE"       "15Q LOSS CNV" "15Q LOSS WILD-TYPE" 
        TCGA-D7-6521         TCGA-D7-6522         TCGA-D7-6524 
"15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" 
        TCGA-D7-6525         TCGA-D7-6526         TCGA-D7-6527 
"15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE"       "15Q LOSS CNV" 
        TCGA-D7-6528         TCGA-D7-6815         TCGA-D7-6817 
      "15Q LOSS CNV" "15Q LOSS WILD-TYPE"       "15Q LOSS CNV" 
        TCGA-D7-6818         TCGA-D7-6820         TCGA-D7-6822 
"15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" 
        TCGA-EQ-5647         TCGA-EQ-8122         TCGA-F1-6177 
"15Q LOSS WILD-TYPE"       "15Q LOSS CNV" "15Q LOSS WILD-TYPE" 
        TCGA-F1-6874         TCGA-F1-6875         TCGA-FP-7735 
"15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" 
        TCGA-FP-7829         TCGA-FP-7916         TCGA-FP-7998 
"15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" 
        TCGA-FP-8099         TCGA-FP-8209         TCGA-FP-8210 
"15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" 
        TCGA-FP-8631         TCGA-HJ-7597         TCGA-IN-7806 
"15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" 
        TCGA-IN-7808         TCGA-IP-7968 
"15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" 
[1] "hr=" "1"  
D62V2, continuous
D62V3, binary
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  15Q LOSS CNV          7    9
  15Q LOSS WILD-TYPE   65   99
        clus
vv       15Q LOSS CNV 15Q LOSS WILD-TYPE
  FEMALE            7                 65
  MALE              9                 99
                    vv
clus                 STOMACH  ADENOCARCINOMA  DIFFUSE TYPE
  15Q LOSS CNV                                           0
  15Q LOSS WILD-TYPE                                    10
                    vv
clus                 STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  15Q LOSS CNV                                                            3
  15Q LOSS WILD-TYPE                                                     13
                    vv
clus                 STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  15Q LOSS CNV                                                                       2
  15Q LOSS WILD-TYPE                                                                 6
                    vv
clus                 STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE
  15Q LOSS CNV                                                              0
  15Q LOSS WILD-TYPE                                                        3
                    vv
clus                 STOMACH ADENOCARCINOMA  SIGNET RING TYPE
  15Q LOSS CNV                                              0
  15Q LOSS WILD-TYPE                                        1
                    vv
clus                 STOMACH ADENOCARCINOMA - DIFFUSE TYPE
  15Q LOSS CNV                                           2
  15Q LOSS WILD-TYPE                                    14
                    vv
clus                 STOMACH ADENOCARCINOMA - NOT OTHERWISE SPECIFIED (NOS)
  15Q LOSS CNV                                                            2
  15Q LOSS WILD-TYPE                                                     71
                    vv
clus                 STOMACH INTESTINAL ADENOCARCINOMA - MUCINOUS TYPE
  15Q LOSS CNV                                                       0
  15Q LOSS WILD-TYPE                                                 7
                    vv
clus                 STOMACH INTESTINAL ADENOCARCINOMA - PAPILLARY TYPE
  15Q LOSS CNV                                                        1
  15Q LOSS WILD-TYPE                                                  2
                    vv
clus                 STOMACH INTESTINAL ADENOCARCINOMA - TUBULAR TYPE
  15Q LOSS CNV                                                      3
  15Q LOSS WILD-TYPE                                                7
                    vv
clus                 STOMACH INTESTINAL ADENOCARCINOMA - TYPE NOT OTHERWISE SPECIFIED (NOS)
  15Q LOSS CNV                                                                            3
  15Q LOSS WILD-TYPE                                                                     25
D62V4, multiclass
                    vv
clus                 T1 T2 T3 T4
  15Q LOSS CNV        0  8  3  0
  15Q LOSS WILD-TYPE  6 44 53 18
D62V5, multiclass
    clus
vv   15Q LOSS CNV 15Q LOSS WILD-TYPE
  T1            0                  6
  T2            8                 44
  T3            3                 53
  T4            0                 18
                    vv
clus                 N0 N1 N2 N3
  15Q LOSS CNV        5  3  0  2
  15Q LOSS WILD-TYPE 39 46 23 13
D62V6, multiclass
    clus
vv   15Q LOSS CNV 15Q LOSS WILD-TYPE
  N0            5                 39
  N1            3                 46
  N2            0                 23
  N3            2                 13
                    vv
clus                  M0  M1  MX
  15Q LOSS CNV         9   1   1
  15Q LOSS WILD-TYPE 109  15   7
D62V7, multiclass
    clus
vv   15Q LOSS CNV 15Q LOSS WILD-TYPE
  M0            9                109
  M1            1                 15
  MX            1                  7
                    vv
clus                  I II III IV
  15Q LOSS CNV        4  2   3  1
  15Q LOSS WILD-TYPE 20 35  36 25
D62V8, multiclass
     clus
vv    15Q LOSS CNV 15Q LOSS WILD-TYPE
  I              4                 20
  II             2                 35
  III            3                 36
  IV             1                 25
D62V9, binary
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  15Q LOSS CNV          2   14
  15Q LOSS WILD-TYPE    3  161
     clus
vv    15Q LOSS CNV 15Q LOSS WILD-TYPE
  NO             2                  3
  YES           14                161
                    vv
clus                  R0  R1  R2  RX
  15Q LOSS CNV        12   1   1   1
  15Q LOSS WILD-TYPE 113   6  11  24
D62V10, multiclass
    clus
vv   15Q LOSS CNV 15Q LOSS WILD-TYPE
  R0           12                113
  R1            1                  6
  R2            1                 11
  RX            1                 24
D62V11, continuous

Clustering(63) Variable = 16p loss
D63V1, survival
                    sevent
clus2                  0   1
  16P LOSS CNV        11   1
  16P LOSS WILD-TYPE 113  18
      16P LOSS CNV 16P LOSS WILD-TYPE 
                12                131 
      16P LOSS CNV 16P LOSS WILD-TYPE 
                 1                 18 
$`16P LOSS CNV`
TCGA-BR-7715 TCGA-BR-7959 TCGA-BR-8060 TCGA-BR-8077 TCGA-BR-8286 TCGA-BR-A4PF 
        1.05         1.08         1.32         0.69         0.43         0.72 
TCGA-BR-A4QI TCGA-CG-4443 TCGA-CG-4449 TCGA-CG-5724 TCGA-D7-6519 TCGA-D7-6822 
        0.49        29.98        19.07        12.03        15.65         4.27 

$`16P LOSS WILD-TYPE`
TCGA-B7-5816 TCGA-B7-5818 TCGA-BR-6452 TCGA-BR-6455 TCGA-BR-6457 TCGA-BR-6458 
        5.62         0.10         0.95         1.41         1.35         1.35 
TCGA-BR-6563 TCGA-BR-6564 TCGA-BR-6565 TCGA-BR-6566 TCGA-BR-6705 TCGA-BR-6706 
        0.85         0.82         0.62         0.62         1.71         2.17 
TCGA-BR-6707 TCGA-BR-6709 TCGA-BR-6710 TCGA-BR-6801 TCGA-BR-6802 TCGA-BR-6803 
        0.99         1.22         0.66         1.12         0.76         0.66 
TCGA-BR-6852 TCGA-BR-7196 TCGA-BR-7197 TCGA-BR-7703 TCGA-BR-7704 TCGA-BR-7707 
        0.26         1.22         1.48         0.46         1.25         0.13 
TCGA-BR-7716 TCGA-BR-7717 TCGA-BR-7722 TCGA-BR-7723 TCGA-BR-7851 TCGA-BR-7901 
        0.82         0.69         0.16         4.54         0.99         0.95 
TCGA-BR-7957 TCGA-BR-7958 TCGA-BR-8059 TCGA-BR-8078 TCGA-BR-8080 TCGA-BR-8081 
        0.69         0.16         0.82         0.95         0.49         0.46 
TCGA-BR-8284 TCGA-BR-8285 TCGA-BR-8289 TCGA-BR-8291 TCGA-BR-8295 TCGA-BR-8296 
        0.72         0.26         0.26         1.18         1.55         1.48 
TCGA-BR-8297 TCGA-BR-8592 TCGA-BR-A4IU TCGA-BR-A4IV TCGA-BR-A4IY TCGA-BR-A4IZ 
        0.76         0.20         0.59         0.92         0.39         0.79 
TCGA-BR-A4J1 TCGA-BR-A4J2 TCGA-BR-A4J4 TCGA-BR-A4J5 TCGA-BR-A4J6 TCGA-BR-A4J8 
        0.72         0.79         0.53         0.43         0.13         0.23 
TCGA-BR-A4J9 TCGA-BR-A4QL TCGA-CD-5798 TCGA-CD-5799 TCGA-CD-5800 TCGA-CD-5801 
        0.10         2.24         0.82         0.69         0.36         0.49 
TCGA-CD-5802 TCGA-CD-5803 TCGA-CG-4300 TCGA-CG-4301 TCGA-CG-4304 TCGA-CG-4305 
        0.30         0.07        20.02         3.02        27.02        15.95 
TCGA-CG-4306 TCGA-CG-4436 TCGA-CG-4437 TCGA-CG-4438 TCGA-CG-4440 TCGA-CG-4441 
        1.02        52.96         8.05        54.05         4.01        14.01 
TCGA-CG-4444 TCGA-CG-4455 TCGA-CG-4460 TCGA-CG-4462 TCGA-CG-4465 TCGA-CG-4466 
       47.05        12.03        21.99         1.02         8.98        18.94 
TCGA-CG-4469 TCGA-CG-4472 TCGA-CG-4474 TCGA-CG-4477 TCGA-CG-5716 TCGA-CG-5717 
        7.07        12.00         1.02         1.02         1.02         6.94 
TCGA-CG-5718 TCGA-CG-5719 TCGA-CG-5720 TCGA-CG-5721 TCGA-CG-5722 TCGA-CG-5723 
        1.02         1.02         0.99         5.98         0.95        70.06 
TCGA-CG-5725 TCGA-CG-5726 TCGA-CG-5727 TCGA-CG-5728 TCGA-CG-5730 TCGA-CG-5732 
       15.02        28.96        31.04        65.10         4.01        55.04 
TCGA-CG-5733 TCGA-CG-5734 TCGA-D7-5577 TCGA-D7-5578 TCGA-D7-5579 TCGA-D7-6518 
       21.07         7.99         8.65         3.58         4.54         9.80 
TCGA-D7-6520 TCGA-D7-6521 TCGA-D7-6522 TCGA-D7-6524 TCGA-D7-6525 TCGA-D7-6526 
        9.63         8.19         6.90         0.69         5.95         6.61 
TCGA-D7-6527 TCGA-D7-6528 TCGA-D7-6815 TCGA-D7-6817 TCGA-D7-6818 TCGA-D7-6820 
        4.14         1.68         3.65         4.70         4.04         2.93 
TCGA-EQ-5647 TCGA-EQ-8122 TCGA-F1-6177 TCGA-F1-6874 TCGA-F1-6875 TCGA-FP-7735 
        0.62         7.79         6.54         2.01        72.23         0.39 
TCGA-FP-7829 TCGA-FP-7916 TCGA-FP-7998 TCGA-FP-8099 TCGA-FP-8209 TCGA-FP-8210 
        0.20         3.02         3.58         1.02        59.05         5.03 
TCGA-FP-8631 TCGA-HJ-7597 TCGA-IN-7806 TCGA-IN-7808 TCGA-IP-7968 
        0.56        26.43         6.87         3.55         2.53 

      16P LOSS CNV 16P LOSS WILD-TYPE 
              0.43               0.07 
      16P LOSS CNV 16P LOSS WILD-TYPE 
             29.98              72.23 
      16P LOSS CNV 16P LOSS WILD-TYPE 
              1.20               1.25 
[1] "0.4 - 30.0 (1.2)" "0.1 - 72.2 (1.2)"
        TCGA-B7-5816         TCGA-B7-5818         TCGA-BR-6452 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-BR-6455         TCGA-BR-6457         TCGA-BR-6458 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-BR-6563         TCGA-BR-6564         TCGA-BR-6565 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-BR-6566         TCGA-BR-6705         TCGA-BR-6706 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-BR-6707         TCGA-BR-6709         TCGA-BR-6710 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-BR-6801         TCGA-BR-6802         TCGA-BR-6803 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-BR-6852         TCGA-BR-7196         TCGA-BR-7197 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-BR-7703         TCGA-BR-7704         TCGA-BR-7707 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-BR-7715         TCGA-BR-7716         TCGA-BR-7717 
      "16P LOSS CNV" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-BR-7722         TCGA-BR-7723         TCGA-BR-7851 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-BR-7901         TCGA-BR-7957         TCGA-BR-7958 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-BR-7959         TCGA-BR-8059         TCGA-BR-8060 
      "16P LOSS CNV" "16P LOSS WILD-TYPE"       "16P LOSS CNV" 
        TCGA-BR-8077         TCGA-BR-8078         TCGA-BR-8080 
      "16P LOSS CNV" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-BR-8081         TCGA-BR-8284         TCGA-BR-8285 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-BR-8286         TCGA-BR-8289         TCGA-BR-8291 
      "16P LOSS CNV" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-BR-8295         TCGA-BR-8296         TCGA-BR-8297 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-BR-8592         TCGA-BR-A4IU         TCGA-BR-A4IV 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-BR-A4IY         TCGA-BR-A4IZ         TCGA-BR-A4J1 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-BR-A4J2         TCGA-BR-A4J4         TCGA-BR-A4J5 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-BR-A4J6         TCGA-BR-A4J8         TCGA-BR-A4J9 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-BR-A4PF         TCGA-BR-A4QI         TCGA-BR-A4QL 
      "16P LOSS CNV"       "16P LOSS CNV" "16P LOSS WILD-TYPE" 
        TCGA-CD-5798         TCGA-CD-5799         TCGA-CD-5800 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-CD-5801         TCGA-CD-5802         TCGA-CD-5803 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-CG-4300         TCGA-CG-4301         TCGA-CG-4304 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-CG-4305         TCGA-CG-4306         TCGA-CG-4436 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-CG-4437         TCGA-CG-4438         TCGA-CG-4440 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-CG-4441         TCGA-CG-4443         TCGA-CG-4444 
"16P LOSS WILD-TYPE"       "16P LOSS CNV" "16P LOSS WILD-TYPE" 
        TCGA-CG-4449         TCGA-CG-4455         TCGA-CG-4460 
      "16P LOSS CNV" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-CG-4462         TCGA-CG-4465         TCGA-CG-4466 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-CG-4469         TCGA-CG-4472         TCGA-CG-4474 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-CG-4477         TCGA-CG-5716         TCGA-CG-5717 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-CG-5718         TCGA-CG-5719         TCGA-CG-5720 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-CG-5721         TCGA-CG-5722         TCGA-CG-5723 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-CG-5724         TCGA-CG-5725         TCGA-CG-5726 
      "16P LOSS CNV" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-CG-5727         TCGA-CG-5728         TCGA-CG-5730 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-CG-5732         TCGA-CG-5733         TCGA-CG-5734 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-D7-5577         TCGA-D7-5578         TCGA-D7-5579 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-D7-6518         TCGA-D7-6519         TCGA-D7-6520 
"16P LOSS WILD-TYPE"       "16P LOSS CNV" "16P LOSS WILD-TYPE" 
        TCGA-D7-6521         TCGA-D7-6522         TCGA-D7-6524 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-D7-6525         TCGA-D7-6526         TCGA-D7-6527 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-D7-6528         TCGA-D7-6815         TCGA-D7-6817 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-D7-6818         TCGA-D7-6820         TCGA-D7-6822 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE"       "16P LOSS CNV" 
        TCGA-EQ-5647         TCGA-EQ-8122         TCGA-F1-6177 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-F1-6874         TCGA-F1-6875         TCGA-FP-7735 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-FP-7829         TCGA-FP-7916         TCGA-FP-7998 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-FP-8099         TCGA-FP-8209         TCGA-FP-8210 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-FP-8631         TCGA-HJ-7597         TCGA-IN-7806 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-IN-7808         TCGA-IP-7968 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-B7-5816         TCGA-B7-5818         TCGA-BR-6452 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-BR-6455         TCGA-BR-6457         TCGA-BR-6458 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-BR-6563         TCGA-BR-6564         TCGA-BR-6565 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-BR-6566         TCGA-BR-6705         TCGA-BR-6706 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-BR-6707         TCGA-BR-6709         TCGA-BR-6710 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-BR-6801         TCGA-BR-6802         TCGA-BR-6803 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-BR-6852         TCGA-BR-7196         TCGA-BR-7197 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-BR-7703         TCGA-BR-7704         TCGA-BR-7707 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-BR-7715         TCGA-BR-7716         TCGA-BR-7717 
      "16P LOSS CNV" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-BR-7722         TCGA-BR-7723         TCGA-BR-7851 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-BR-7901         TCGA-BR-7957         TCGA-BR-7958 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-BR-7959         TCGA-BR-8059         TCGA-BR-8060 
      "16P LOSS CNV" "16P LOSS WILD-TYPE"       "16P LOSS CNV" 
        TCGA-BR-8077         TCGA-BR-8078         TCGA-BR-8080 
      "16P LOSS CNV" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-BR-8081         TCGA-BR-8284         TCGA-BR-8285 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-BR-8286         TCGA-BR-8289         TCGA-BR-8291 
      "16P LOSS CNV" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-BR-8295         TCGA-BR-8296         TCGA-BR-8297 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-BR-8592         TCGA-BR-A4IU         TCGA-BR-A4IV 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-BR-A4IY         TCGA-BR-A4IZ         TCGA-BR-A4J1 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-BR-A4J2         TCGA-BR-A4J4         TCGA-BR-A4J5 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-BR-A4J6         TCGA-BR-A4J8         TCGA-BR-A4J9 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-BR-A4PF         TCGA-BR-A4QI         TCGA-BR-A4QL 
      "16P LOSS CNV"       "16P LOSS CNV" "16P LOSS WILD-TYPE" 
        TCGA-CD-5798         TCGA-CD-5799         TCGA-CD-5800 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-CD-5801         TCGA-CD-5802         TCGA-CD-5803 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-CG-4300         TCGA-CG-4301         TCGA-CG-4304 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-CG-4305         TCGA-CG-4306         TCGA-CG-4436 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-CG-4437         TCGA-CG-4438         TCGA-CG-4440 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-CG-4441         TCGA-CG-4443         TCGA-CG-4444 
"16P LOSS WILD-TYPE"       "16P LOSS CNV" "16P LOSS WILD-TYPE" 
        TCGA-CG-4449         TCGA-CG-4455         TCGA-CG-4460 
      "16P LOSS CNV" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-CG-4462         TCGA-CG-4465         TCGA-CG-4466 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-CG-4469         TCGA-CG-4472         TCGA-CG-4474 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-CG-4477         TCGA-CG-5716         TCGA-CG-5717 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-CG-5718         TCGA-CG-5719         TCGA-CG-5720 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-CG-5721         TCGA-CG-5722         TCGA-CG-5723 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-CG-5724         TCGA-CG-5725         TCGA-CG-5726 
      "16P LOSS CNV" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-CG-5727         TCGA-CG-5728         TCGA-CG-5730 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-CG-5732         TCGA-CG-5733         TCGA-CG-5734 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-D7-5577         TCGA-D7-5578         TCGA-D7-5579 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-D7-6518         TCGA-D7-6519         TCGA-D7-6520 
"16P LOSS WILD-TYPE"       "16P LOSS CNV" "16P LOSS WILD-TYPE" 
        TCGA-D7-6521         TCGA-D7-6522         TCGA-D7-6524 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-D7-6525         TCGA-D7-6526         TCGA-D7-6527 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-D7-6528         TCGA-D7-6815         TCGA-D7-6817 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-D7-6818         TCGA-D7-6820         TCGA-D7-6822 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE"       "16P LOSS CNV" 
        TCGA-EQ-5647         TCGA-EQ-8122         TCGA-F1-6177 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-F1-6874         TCGA-F1-6875         TCGA-FP-7735 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-FP-7829         TCGA-FP-7916         TCGA-FP-7998 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-FP-8099         TCGA-FP-8209         TCGA-FP-8210 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-FP-8631         TCGA-HJ-7597         TCGA-IN-7806 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-IN-7808         TCGA-IP-7968 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-B7-5816         TCGA-B7-5818         TCGA-BR-6452 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-BR-6455         TCGA-BR-6457         TCGA-BR-6458 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-BR-6563         TCGA-BR-6564         TCGA-BR-6565 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-BR-6566         TCGA-BR-6705         TCGA-BR-6706 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-BR-6707         TCGA-BR-6709         TCGA-BR-6710 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-BR-6801         TCGA-BR-6802         TCGA-BR-6803 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-BR-6852         TCGA-BR-7196         TCGA-BR-7197 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-BR-7703         TCGA-BR-7704         TCGA-BR-7707 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-BR-7715         TCGA-BR-7716         TCGA-BR-7717 
      "16P LOSS CNV" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-BR-7722         TCGA-BR-7723         TCGA-BR-7851 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-BR-7901         TCGA-BR-7957         TCGA-BR-7958 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-BR-7959         TCGA-BR-8059         TCGA-BR-8060 
      "16P LOSS CNV" "16P LOSS WILD-TYPE"       "16P LOSS CNV" 
        TCGA-BR-8077         TCGA-BR-8078         TCGA-BR-8080 
      "16P LOSS CNV" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-BR-8081         TCGA-BR-8284         TCGA-BR-8285 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-BR-8286         TCGA-BR-8289         TCGA-BR-8291 
      "16P LOSS CNV" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-BR-8295         TCGA-BR-8296         TCGA-BR-8297 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-BR-8592         TCGA-BR-A4IU         TCGA-BR-A4IV 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-BR-A4IY         TCGA-BR-A4IZ         TCGA-BR-A4J1 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-BR-A4J2         TCGA-BR-A4J4         TCGA-BR-A4J5 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-BR-A4J6         TCGA-BR-A4J8         TCGA-BR-A4J9 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-BR-A4PF         TCGA-BR-A4QI         TCGA-BR-A4QL 
      "16P LOSS CNV"       "16P LOSS CNV" "16P LOSS WILD-TYPE" 
        TCGA-CD-5798         TCGA-CD-5799         TCGA-CD-5800 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-CD-5801         TCGA-CD-5802         TCGA-CD-5803 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-CG-4300         TCGA-CG-4301         TCGA-CG-4304 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-CG-4305         TCGA-CG-4306         TCGA-CG-4436 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-CG-4437         TCGA-CG-4438         TCGA-CG-4440 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-CG-4441         TCGA-CG-4443         TCGA-CG-4444 
"16P LOSS WILD-TYPE"       "16P LOSS CNV" "16P LOSS WILD-TYPE" 
        TCGA-CG-4449         TCGA-CG-4455         TCGA-CG-4460 
      "16P LOSS CNV" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-CG-4462         TCGA-CG-4465         TCGA-CG-4466 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-CG-4469         TCGA-CG-4472         TCGA-CG-4474 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-CG-4477         TCGA-CG-5716         TCGA-CG-5717 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-CG-5718         TCGA-CG-5719         TCGA-CG-5720 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-CG-5721         TCGA-CG-5722         TCGA-CG-5723 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-CG-5724         TCGA-CG-5725         TCGA-CG-5726 
      "16P LOSS CNV" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-CG-5727         TCGA-CG-5728         TCGA-CG-5730 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-CG-5732         TCGA-CG-5733         TCGA-CG-5734 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-D7-5577         TCGA-D7-5578         TCGA-D7-5579 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-D7-6518         TCGA-D7-6519         TCGA-D7-6520 
"16P LOSS WILD-TYPE"       "16P LOSS CNV" "16P LOSS WILD-TYPE" 
        TCGA-D7-6521         TCGA-D7-6522         TCGA-D7-6524 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-D7-6525         TCGA-D7-6526         TCGA-D7-6527 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-D7-6528         TCGA-D7-6815         TCGA-D7-6817 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-D7-6818         TCGA-D7-6820         TCGA-D7-6822 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE"       "16P LOSS CNV" 
        TCGA-EQ-5647         TCGA-EQ-8122         TCGA-F1-6177 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-F1-6874         TCGA-F1-6875         TCGA-FP-7735 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-FP-7829         TCGA-FP-7916         TCGA-FP-7998 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-FP-8099         TCGA-FP-8209         TCGA-FP-8210 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-FP-8631         TCGA-HJ-7597         TCGA-IN-7806 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-IN-7808         TCGA-IP-7968 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
[1] "hr=" "1.9"
D63V2, continuous
D63V3, binary
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  16P LOSS CNV          5   11
  16P LOSS WILD-TYPE   67   97
        clus
vv       16P LOSS CNV 16P LOSS WILD-TYPE
  FEMALE            5                 67
  MALE             11                 97
                    vv
clus                 STOMACH  ADENOCARCINOMA  DIFFUSE TYPE
  16P LOSS CNV                                           0
  16P LOSS WILD-TYPE                                    10
                    vv
clus                 STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  16P LOSS CNV                                                            4
  16P LOSS WILD-TYPE                                                     12
                    vv
clus                 STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  16P LOSS CNV                                                                       1
  16P LOSS WILD-TYPE                                                                 7
                    vv
clus                 STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE
  16P LOSS CNV                                                              1
  16P LOSS WILD-TYPE                                                        2
                    vv
clus                 STOMACH ADENOCARCINOMA  SIGNET RING TYPE
  16P LOSS CNV                                              0
  16P LOSS WILD-TYPE                                        1
                    vv
clus                 STOMACH ADENOCARCINOMA - DIFFUSE TYPE
  16P LOSS CNV                                           2
  16P LOSS WILD-TYPE                                    14
                    vv
clus                 STOMACH ADENOCARCINOMA - NOT OTHERWISE SPECIFIED (NOS)
  16P LOSS CNV                                                            3
  16P LOSS WILD-TYPE                                                     70
                    vv
clus                 STOMACH INTESTINAL ADENOCARCINOMA - MUCINOUS TYPE
  16P LOSS CNV                                                       2
  16P LOSS WILD-TYPE                                                 5
                    vv
clus                 STOMACH INTESTINAL ADENOCARCINOMA - PAPILLARY TYPE
  16P LOSS CNV                                                        0
  16P LOSS WILD-TYPE                                                  3
                    vv
clus                 STOMACH INTESTINAL ADENOCARCINOMA - TUBULAR TYPE
  16P LOSS CNV                                                      2
  16P LOSS WILD-TYPE                                                8
                    vv
clus                 STOMACH INTESTINAL ADENOCARCINOMA - TYPE NOT OTHERWISE SPECIFIED (NOS)
  16P LOSS CNV                                                                            1
  16P LOSS WILD-TYPE                                                                     27
D63V4, multiclass
                    vv
clus                 T1 T2 T3 T4
  16P LOSS CNV        1  5  3  0
  16P LOSS WILD-TYPE  5 47 53 18
D63V5, multiclass
    clus
vv   16P LOSS CNV 16P LOSS WILD-TYPE
  T1            1                  5
  T2            5                 47
  T3            3                 53
  T4            0                 18
                    vv
clus                 N0 N1 N2 N3
  16P LOSS CNV        3  3  0  2
  16P LOSS WILD-TYPE 41 46 23 13
D63V6, multiclass
    clus
vv   16P LOSS CNV 16P LOSS WILD-TYPE
  N0            3                 41
  N1            3                 46
  N2            0                 23
  N3            2                 13
                    vv
clus                  M0  M1  MX
  16P LOSS CNV         9   1   0
  16P LOSS WILD-TYPE 109  15   8
D63V7, multiclass
    clus
vv   16P LOSS CNV 16P LOSS WILD-TYPE
  M0            9                109
  M1            1                 15
  MX            0                  8
                    vv
clus                  I II III IV
  16P LOSS CNV        2  2   2  2
  16P LOSS WILD-TYPE 22 35  37 24
D63V8, multiclass
     clus
vv    16P LOSS CNV 16P LOSS WILD-TYPE
  I              2                 22
  II             2                 35
  III            2                 37
  IV             2                 24
D63V9, binary
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  16P LOSS CNV          1   15
  16P LOSS WILD-TYPE    4  160
     clus
vv    16P LOSS CNV 16P LOSS WILD-TYPE
  NO             1                  4
  YES           15                160
                    vv
clus                  R0  R1  R2  RX
  16P LOSS CNV        11   2   1   2
  16P LOSS WILD-TYPE 114   5  11  23
D63V10, multiclass
    clus
vv   16P LOSS CNV 16P LOSS WILD-TYPE
  R0           11                114
  R1            2                  5
  R2            1                 11
  RX            2                 23
D63V11, continuous

Clustering(64) Variable = 16q loss
D64V1, survival
                    sevent
clus2                  0   1
  16Q LOSS CNV        13   1
  16Q LOSS WILD-TYPE 111  18
      16Q LOSS CNV 16Q LOSS WILD-TYPE 
                14                129 
      16Q LOSS CNV 16Q LOSS WILD-TYPE 
                 1                 18 
$`16Q LOSS CNV`
TCGA-BR-7715 TCGA-BR-7959 TCGA-BR-8060 TCGA-BR-8077 TCGA-BR-8286 TCGA-BR-A4PF 
        1.05         1.08         1.32         0.69         0.43         0.72 
TCGA-BR-A4QI TCGA-CD-5802 TCGA-CG-4443 TCGA-CG-4449 TCGA-CG-4477 TCGA-CG-5724 
        0.49         0.30        29.98        19.07         1.02        12.03 
TCGA-D7-6519 TCGA-D7-6817 
       15.65         4.70 

$`16Q LOSS WILD-TYPE`
TCGA-B7-5816 TCGA-B7-5818 TCGA-BR-6452 TCGA-BR-6455 TCGA-BR-6457 TCGA-BR-6458 
        5.62         0.10         0.95         1.41         1.35         1.35 
TCGA-BR-6563 TCGA-BR-6564 TCGA-BR-6565 TCGA-BR-6566 TCGA-BR-6705 TCGA-BR-6706 
        0.85         0.82         0.62         0.62         1.71         2.17 
TCGA-BR-6707 TCGA-BR-6709 TCGA-BR-6710 TCGA-BR-6801 TCGA-BR-6802 TCGA-BR-6803 
        0.99         1.22         0.66         1.12         0.76         0.66 
TCGA-BR-6852 TCGA-BR-7196 TCGA-BR-7197 TCGA-BR-7703 TCGA-BR-7704 TCGA-BR-7707 
        0.26         1.22         1.48         0.46         1.25         0.13 
TCGA-BR-7716 TCGA-BR-7717 TCGA-BR-7722 TCGA-BR-7723 TCGA-BR-7851 TCGA-BR-7901 
        0.82         0.69         0.16         4.54         0.99         0.95 
TCGA-BR-7957 TCGA-BR-7958 TCGA-BR-8059 TCGA-BR-8078 TCGA-BR-8080 TCGA-BR-8081 
        0.69         0.16         0.82         0.95         0.49         0.46 
TCGA-BR-8284 TCGA-BR-8285 TCGA-BR-8289 TCGA-BR-8291 TCGA-BR-8295 TCGA-BR-8296 
        0.72         0.26         0.26         1.18         1.55         1.48 
TCGA-BR-8297 TCGA-BR-8592 TCGA-BR-A4IU TCGA-BR-A4IV TCGA-BR-A4IY TCGA-BR-A4IZ 
        0.76         0.20         0.59         0.92         0.39         0.79 
TCGA-BR-A4J1 TCGA-BR-A4J2 TCGA-BR-A4J4 TCGA-BR-A4J5 TCGA-BR-A4J6 TCGA-BR-A4J8 
        0.72         0.79         0.53         0.43         0.13         0.23 
TCGA-BR-A4J9 TCGA-BR-A4QL TCGA-CD-5798 TCGA-CD-5799 TCGA-CD-5800 TCGA-CD-5801 
        0.10         2.24         0.82         0.69         0.36         0.49 
TCGA-CD-5803 TCGA-CG-4300 TCGA-CG-4301 TCGA-CG-4304 TCGA-CG-4305 TCGA-CG-4306 
        0.07        20.02         3.02        27.02        15.95         1.02 
TCGA-CG-4436 TCGA-CG-4437 TCGA-CG-4438 TCGA-CG-4440 TCGA-CG-4441 TCGA-CG-4444 
       52.96         8.05        54.05         4.01        14.01        47.05 
TCGA-CG-4455 TCGA-CG-4460 TCGA-CG-4462 TCGA-CG-4465 TCGA-CG-4466 TCGA-CG-4469 
       12.03        21.99         1.02         8.98        18.94         7.07 
TCGA-CG-4472 TCGA-CG-4474 TCGA-CG-5716 TCGA-CG-5717 TCGA-CG-5718 TCGA-CG-5719 
       12.00         1.02         1.02         6.94         1.02         1.02 
TCGA-CG-5720 TCGA-CG-5721 TCGA-CG-5722 TCGA-CG-5723 TCGA-CG-5725 TCGA-CG-5726 
        0.99         5.98         0.95        70.06        15.02        28.96 
TCGA-CG-5727 TCGA-CG-5728 TCGA-CG-5730 TCGA-CG-5732 TCGA-CG-5733 TCGA-CG-5734 
       31.04        65.10         4.01        55.04        21.07         7.99 
TCGA-D7-5577 TCGA-D7-5578 TCGA-D7-5579 TCGA-D7-6518 TCGA-D7-6520 TCGA-D7-6521 
        8.65         3.58         4.54         9.80         9.63         8.19 
TCGA-D7-6522 TCGA-D7-6524 TCGA-D7-6525 TCGA-D7-6526 TCGA-D7-6527 TCGA-D7-6528 
        6.90         0.69         5.95         6.61         4.14         1.68 
TCGA-D7-6815 TCGA-D7-6818 TCGA-D7-6820 TCGA-D7-6822 TCGA-EQ-5647 TCGA-EQ-8122 
        3.65         4.04         2.93         4.27         0.62         7.79 
TCGA-F1-6177 TCGA-F1-6874 TCGA-F1-6875 TCGA-FP-7735 TCGA-FP-7829 TCGA-FP-7916 
        6.54         2.01        72.23         0.39         0.20         3.02 
TCGA-FP-7998 TCGA-FP-8099 TCGA-FP-8209 TCGA-FP-8210 TCGA-FP-8631 TCGA-HJ-7597 
        3.58         1.02        59.05         5.03         0.56        26.43 
TCGA-IN-7806 TCGA-IN-7808 TCGA-IP-7968 
        6.87         3.55         2.53 

      16Q LOSS CNV 16Q LOSS WILD-TYPE 
              0.30               0.07 
      16Q LOSS CNV 16Q LOSS WILD-TYPE 
             29.98              72.23 
      16Q LOSS CNV 16Q LOSS WILD-TYPE 
             1.065              1.350 
[1] "0.3 - 30.0 (1.1)" "0.1 - 72.2 (1.4)"
        TCGA-B7-5816         TCGA-B7-5818         TCGA-BR-6452 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-BR-6455         TCGA-BR-6457         TCGA-BR-6458 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-BR-6563         TCGA-BR-6564         TCGA-BR-6565 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-BR-6566         TCGA-BR-6705         TCGA-BR-6706 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-BR-6707         TCGA-BR-6709         TCGA-BR-6710 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-BR-6801         TCGA-BR-6802         TCGA-BR-6803 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-BR-6852         TCGA-BR-7196         TCGA-BR-7197 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-BR-7703         TCGA-BR-7704         TCGA-BR-7707 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-BR-7715         TCGA-BR-7716         TCGA-BR-7717 
      "16Q LOSS CNV" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-BR-7722         TCGA-BR-7723         TCGA-BR-7851 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-BR-7901         TCGA-BR-7957         TCGA-BR-7958 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-BR-7959         TCGA-BR-8059         TCGA-BR-8060 
      "16Q LOSS CNV" "16Q LOSS WILD-TYPE"       "16Q LOSS CNV" 
        TCGA-BR-8077         TCGA-BR-8078         TCGA-BR-8080 
      "16Q LOSS CNV" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-BR-8081         TCGA-BR-8284         TCGA-BR-8285 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-BR-8286         TCGA-BR-8289         TCGA-BR-8291 
      "16Q LOSS CNV" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-BR-8295         TCGA-BR-8296         TCGA-BR-8297 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-BR-8592         TCGA-BR-A4IU         TCGA-BR-A4IV 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-BR-A4IY         TCGA-BR-A4IZ         TCGA-BR-A4J1 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-BR-A4J2         TCGA-BR-A4J4         TCGA-BR-A4J5 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-BR-A4J6         TCGA-BR-A4J8         TCGA-BR-A4J9 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-BR-A4PF         TCGA-BR-A4QI         TCGA-BR-A4QL 
      "16Q LOSS CNV"       "16Q LOSS CNV" "16Q LOSS WILD-TYPE" 
        TCGA-CD-5798         TCGA-CD-5799         TCGA-CD-5800 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-CD-5801         TCGA-CD-5802         TCGA-CD-5803 
"16Q LOSS WILD-TYPE"       "16Q LOSS CNV" "16Q LOSS WILD-TYPE" 
        TCGA-CG-4300         TCGA-CG-4301         TCGA-CG-4304 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-CG-4305         TCGA-CG-4306         TCGA-CG-4436 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-CG-4437         TCGA-CG-4438         TCGA-CG-4440 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-CG-4441         TCGA-CG-4443         TCGA-CG-4444 
"16Q LOSS WILD-TYPE"       "16Q LOSS CNV" "16Q LOSS WILD-TYPE" 
        TCGA-CG-4449         TCGA-CG-4455         TCGA-CG-4460 
      "16Q LOSS CNV" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-CG-4462         TCGA-CG-4465         TCGA-CG-4466 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-CG-4469         TCGA-CG-4472         TCGA-CG-4474 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-CG-4477         TCGA-CG-5716         TCGA-CG-5717 
      "16Q LOSS CNV" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-CG-5718         TCGA-CG-5719         TCGA-CG-5720 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-CG-5721         TCGA-CG-5722         TCGA-CG-5723 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-CG-5724         TCGA-CG-5725         TCGA-CG-5726 
      "16Q LOSS CNV" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-CG-5727         TCGA-CG-5728         TCGA-CG-5730 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-CG-5732         TCGA-CG-5733         TCGA-CG-5734 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-D7-5577         TCGA-D7-5578         TCGA-D7-5579 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-D7-6518         TCGA-D7-6519         TCGA-D7-6520 
"16Q LOSS WILD-TYPE"       "16Q LOSS CNV" "16Q LOSS WILD-TYPE" 
        TCGA-D7-6521         TCGA-D7-6522         TCGA-D7-6524 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-D7-6525         TCGA-D7-6526         TCGA-D7-6527 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-D7-6528         TCGA-D7-6815         TCGA-D7-6817 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE"       "16Q LOSS CNV" 
        TCGA-D7-6818         TCGA-D7-6820         TCGA-D7-6822 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-EQ-5647         TCGA-EQ-8122         TCGA-F1-6177 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-F1-6874         TCGA-F1-6875         TCGA-FP-7735 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-FP-7829         TCGA-FP-7916         TCGA-FP-7998 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-FP-8099         TCGA-FP-8209         TCGA-FP-8210 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-FP-8631         TCGA-HJ-7597         TCGA-IN-7806 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-IN-7808         TCGA-IP-7968 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-B7-5816         TCGA-B7-5818         TCGA-BR-6452 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-BR-6455         TCGA-BR-6457         TCGA-BR-6458 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-BR-6563         TCGA-BR-6564         TCGA-BR-6565 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-BR-6566         TCGA-BR-6705         TCGA-BR-6706 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-BR-6707         TCGA-BR-6709         TCGA-BR-6710 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-BR-6801         TCGA-BR-6802         TCGA-BR-6803 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-BR-6852         TCGA-BR-7196         TCGA-BR-7197 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-BR-7703         TCGA-BR-7704         TCGA-BR-7707 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-BR-7715         TCGA-BR-7716         TCGA-BR-7717 
      "16Q LOSS CNV" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-BR-7722         TCGA-BR-7723         TCGA-BR-7851 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-BR-7901         TCGA-BR-7957         TCGA-BR-7958 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-BR-7959         TCGA-BR-8059         TCGA-BR-8060 
      "16Q LOSS CNV" "16Q LOSS WILD-TYPE"       "16Q LOSS CNV" 
        TCGA-BR-8077         TCGA-BR-8078         TCGA-BR-8080 
      "16Q LOSS CNV" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-BR-8081         TCGA-BR-8284         TCGA-BR-8285 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-BR-8286         TCGA-BR-8289         TCGA-BR-8291 
      "16Q LOSS CNV" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-BR-8295         TCGA-BR-8296         TCGA-BR-8297 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-BR-8592         TCGA-BR-A4IU         TCGA-BR-A4IV 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-BR-A4IY         TCGA-BR-A4IZ         TCGA-BR-A4J1 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-BR-A4J2         TCGA-BR-A4J4         TCGA-BR-A4J5 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-BR-A4J6         TCGA-BR-A4J8         TCGA-BR-A4J9 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-BR-A4PF         TCGA-BR-A4QI         TCGA-BR-A4QL 
      "16Q LOSS CNV"       "16Q LOSS CNV" "16Q LOSS WILD-TYPE" 
        TCGA-CD-5798         TCGA-CD-5799         TCGA-CD-5800 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-CD-5801         TCGA-CD-5802         TCGA-CD-5803 
"16Q LOSS WILD-TYPE"       "16Q LOSS CNV" "16Q LOSS WILD-TYPE" 
        TCGA-CG-4300         TCGA-CG-4301         TCGA-CG-4304 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-CG-4305         TCGA-CG-4306         TCGA-CG-4436 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-CG-4437         TCGA-CG-4438         TCGA-CG-4440 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-CG-4441         TCGA-CG-4443         TCGA-CG-4444 
"16Q LOSS WILD-TYPE"       "16Q LOSS CNV" "16Q LOSS WILD-TYPE" 
        TCGA-CG-4449         TCGA-CG-4455         TCGA-CG-4460 
      "16Q LOSS CNV" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-CG-4462         TCGA-CG-4465         TCGA-CG-4466 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-CG-4469         TCGA-CG-4472         TCGA-CG-4474 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-CG-4477         TCGA-CG-5716         TCGA-CG-5717 
      "16Q LOSS CNV" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-CG-5718         TCGA-CG-5719         TCGA-CG-5720 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-CG-5721         TCGA-CG-5722         TCGA-CG-5723 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-CG-5724         TCGA-CG-5725         TCGA-CG-5726 
      "16Q LOSS CNV" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-CG-5727         TCGA-CG-5728         TCGA-CG-5730 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-CG-5732         TCGA-CG-5733         TCGA-CG-5734 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-D7-5577         TCGA-D7-5578         TCGA-D7-5579 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-D7-6518         TCGA-D7-6519         TCGA-D7-6520 
"16Q LOSS WILD-TYPE"       "16Q LOSS CNV" "16Q LOSS WILD-TYPE" 
        TCGA-D7-6521         TCGA-D7-6522         TCGA-D7-6524 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-D7-6525         TCGA-D7-6526         TCGA-D7-6527 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-D7-6528         TCGA-D7-6815         TCGA-D7-6817 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE"       "16Q LOSS CNV" 
        TCGA-D7-6818         TCGA-D7-6820         TCGA-D7-6822 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-EQ-5647         TCGA-EQ-8122         TCGA-F1-6177 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-F1-6874         TCGA-F1-6875         TCGA-FP-7735 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-FP-7829         TCGA-FP-7916         TCGA-FP-7998 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-FP-8099         TCGA-FP-8209         TCGA-FP-8210 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-FP-8631         TCGA-HJ-7597         TCGA-IN-7806 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-IN-7808         TCGA-IP-7968 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-B7-5816         TCGA-B7-5818         TCGA-BR-6452 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-BR-6455         TCGA-BR-6457         TCGA-BR-6458 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-BR-6563         TCGA-BR-6564         TCGA-BR-6565 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-BR-6566         TCGA-BR-6705         TCGA-BR-6706 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-BR-6707         TCGA-BR-6709         TCGA-BR-6710 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-BR-6801         TCGA-BR-6802         TCGA-BR-6803 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-BR-6852         TCGA-BR-7196         TCGA-BR-7197 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-BR-7703         TCGA-BR-7704         TCGA-BR-7707 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-BR-7715         TCGA-BR-7716         TCGA-BR-7717 
      "16Q LOSS CNV" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-BR-7722         TCGA-BR-7723         TCGA-BR-7851 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-BR-7901         TCGA-BR-7957         TCGA-BR-7958 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-BR-7959         TCGA-BR-8059         TCGA-BR-8060 
      "16Q LOSS CNV" "16Q LOSS WILD-TYPE"       "16Q LOSS CNV" 
        TCGA-BR-8077         TCGA-BR-8078         TCGA-BR-8080 
      "16Q LOSS CNV" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-BR-8081         TCGA-BR-8284         TCGA-BR-8285 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-BR-8286         TCGA-BR-8289         TCGA-BR-8291 
      "16Q LOSS CNV" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-BR-8295         TCGA-BR-8296         TCGA-BR-8297 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-BR-8592         TCGA-BR-A4IU         TCGA-BR-A4IV 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-BR-A4IY         TCGA-BR-A4IZ         TCGA-BR-A4J1 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-BR-A4J2         TCGA-BR-A4J4         TCGA-BR-A4J5 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-BR-A4J6         TCGA-BR-A4J8         TCGA-BR-A4J9 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-BR-A4PF         TCGA-BR-A4QI         TCGA-BR-A4QL 
      "16Q LOSS CNV"       "16Q LOSS CNV" "16Q LOSS WILD-TYPE" 
        TCGA-CD-5798         TCGA-CD-5799         TCGA-CD-5800 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-CD-5801         TCGA-CD-5802         TCGA-CD-5803 
"16Q LOSS WILD-TYPE"       "16Q LOSS CNV" "16Q LOSS WILD-TYPE" 
        TCGA-CG-4300         TCGA-CG-4301         TCGA-CG-4304 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-CG-4305         TCGA-CG-4306         TCGA-CG-4436 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-CG-4437         TCGA-CG-4438         TCGA-CG-4440 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-CG-4441         TCGA-CG-4443         TCGA-CG-4444 
"16Q LOSS WILD-TYPE"       "16Q LOSS CNV" "16Q LOSS WILD-TYPE" 
        TCGA-CG-4449         TCGA-CG-4455         TCGA-CG-4460 
      "16Q LOSS CNV" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-CG-4462         TCGA-CG-4465         TCGA-CG-4466 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-CG-4469         TCGA-CG-4472         TCGA-CG-4474 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-CG-4477         TCGA-CG-5716         TCGA-CG-5717 
      "16Q LOSS CNV" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-CG-5718         TCGA-CG-5719         TCGA-CG-5720 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-CG-5721         TCGA-CG-5722         TCGA-CG-5723 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-CG-5724         TCGA-CG-5725         TCGA-CG-5726 
      "16Q LOSS CNV" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-CG-5727         TCGA-CG-5728         TCGA-CG-5730 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-CG-5732         TCGA-CG-5733         TCGA-CG-5734 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-D7-5577         TCGA-D7-5578         TCGA-D7-5579 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-D7-6518         TCGA-D7-6519         TCGA-D7-6520 
"16Q LOSS WILD-TYPE"       "16Q LOSS CNV" "16Q LOSS WILD-TYPE" 
        TCGA-D7-6521         TCGA-D7-6522         TCGA-D7-6524 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-D7-6525         TCGA-D7-6526         TCGA-D7-6527 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-D7-6528         TCGA-D7-6815         TCGA-D7-6817 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE"       "16Q LOSS CNV" 
        TCGA-D7-6818         TCGA-D7-6820         TCGA-D7-6822 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-EQ-5647         TCGA-EQ-8122         TCGA-F1-6177 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-F1-6874         TCGA-F1-6875         TCGA-FP-7735 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-FP-7829         TCGA-FP-7916         TCGA-FP-7998 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-FP-8099         TCGA-FP-8209         TCGA-FP-8210 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-FP-8631         TCGA-HJ-7597         TCGA-IN-7806 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-IN-7808         TCGA-IP-7968 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
[1] "hr=" "1.9"
D64V2, continuous
D64V3, binary
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  16Q LOSS CNV          6   13
  16Q LOSS WILD-TYPE   66   95
        clus
vv       16Q LOSS CNV 16Q LOSS WILD-TYPE
  FEMALE            6                 66
  MALE             13                 95
                    vv
clus                 STOMACH  ADENOCARCINOMA  DIFFUSE TYPE
  16Q LOSS CNV                                           0
  16Q LOSS WILD-TYPE                                    10
                    vv
clus                 STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  16Q LOSS CNV                                                            4
  16Q LOSS WILD-TYPE                                                     12
                    vv
clus                 STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  16Q LOSS CNV                                                                       1
  16Q LOSS WILD-TYPE                                                                 7
                    vv
clus                 STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE
  16Q LOSS CNV                                                              1
  16Q LOSS WILD-TYPE                                                        2
                    vv
clus                 STOMACH ADENOCARCINOMA  SIGNET RING TYPE
  16Q LOSS CNV                                              0
  16Q LOSS WILD-TYPE                                        1
                    vv
clus                 STOMACH ADENOCARCINOMA - DIFFUSE TYPE
  16Q LOSS CNV                                           2
  16Q LOSS WILD-TYPE                                    14
                    vv
clus                 STOMACH ADENOCARCINOMA - NOT OTHERWISE SPECIFIED (NOS)
  16Q LOSS CNV                                                            4
  16Q LOSS WILD-TYPE                                                     69
                    vv
clus                 STOMACH INTESTINAL ADENOCARCINOMA - MUCINOUS TYPE
  16Q LOSS CNV                                                       2
  16Q LOSS WILD-TYPE                                                 5
                    vv
clus                 STOMACH INTESTINAL ADENOCARCINOMA - PAPILLARY TYPE
  16Q LOSS CNV                                                        0
  16Q LOSS WILD-TYPE                                                  3
                    vv
clus                 STOMACH INTESTINAL ADENOCARCINOMA - TUBULAR TYPE
  16Q LOSS CNV                                                      2
  16Q LOSS WILD-TYPE                                                8
                    vv
clus                 STOMACH INTESTINAL ADENOCARCINOMA - TYPE NOT OTHERWISE SPECIFIED (NOS)
  16Q LOSS CNV                                                                            2
  16Q LOSS WILD-TYPE                                                                     26
D64V4, multiclass
                    vv
clus                 T1 T2 T3 T4
  16Q LOSS CNV        1  6  5  0
  16Q LOSS WILD-TYPE  5 46 51 18
D64V5, multiclass
    clus
vv   16Q LOSS CNV 16Q LOSS WILD-TYPE
  T1            1                  5
  T2            6                 46
  T3            5                 51
  T4            0                 18
                    vv
clus                 N0 N1 N2 N3
  16Q LOSS CNV        4  4  0  3
  16Q LOSS WILD-TYPE 40 45 23 12
D64V6, multiclass
    clus
vv   16Q LOSS CNV 16Q LOSS WILD-TYPE
  N0            4                 40
  N1            4                 45
  N2            0                 23
  N3            3                 12
                    vv
clus                  M0  M1  MX
  16Q LOSS CNV        12   1   0
  16Q LOSS WILD-TYPE 106  15   8
D64V7, multiclass
    clus
vv   16Q LOSS CNV 16Q LOSS WILD-TYPE
  M0           12                106
  M1            1                 15
  MX            0                  8
                    vv
clus                  I II III IV
  16Q LOSS CNV        2  4   3  2
  16Q LOSS WILD-TYPE 22 33  36 24
D64V8, multiclass
     clus
vv    16Q LOSS CNV 16Q LOSS WILD-TYPE
  I              2                 22
  II             4                 33
  III            3                 36
  IV             2                 24
D64V9, binary
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  16Q LOSS CNV          1   18
  16Q LOSS WILD-TYPE    4  157
     clus
vv    16Q LOSS CNV 16Q LOSS WILD-TYPE
  NO             1                  4
  YES           18                157
                    vv
clus                  R0  R1  R2  RX
  16Q LOSS CNV        13   2   1   2
  16Q LOSS WILD-TYPE 112   5  11  23
D64V10, multiclass
    clus
vv   16Q LOSS CNV 16Q LOSS WILD-TYPE
  R0           13                112
  R1            2                  5
  R2            1                 11
  RX            2                 23
D64V11, continuous

Clustering(65) Variable = 17p loss
D65V1, survival
                    sevent
clus2                 0  1
  17P LOSS CNV       26  4
  17P LOSS WILD-TYPE 98 15
      17P LOSS CNV 17P LOSS WILD-TYPE 
                30                113 
      17P LOSS CNV 17P LOSS WILD-TYPE 
                 4                 15 
$`17P LOSS CNV`
TCGA-B7-5818 TCGA-BR-7197 TCGA-BR-7715 TCGA-BR-7959 TCGA-BR-8289 TCGA-BR-8296 
        0.10         1.48         1.05         1.08         0.26         1.48 
TCGA-BR-A4J1 TCGA-CD-5799 TCGA-CG-4300 TCGA-CG-4301 TCGA-CG-4304 TCGA-CG-4437 
        0.72         0.69        20.02         3.02        27.02         8.05 
TCGA-CG-4438 TCGA-CG-4440 TCGA-CG-4443 TCGA-CG-4469 TCGA-CG-4477 TCGA-CG-5719 
       54.05         4.01        29.98         7.07         1.02         1.02 
TCGA-CG-5725 TCGA-CG-5727 TCGA-CG-5730 TCGA-D7-6520 TCGA-D7-6521 TCGA-D7-6526 
       15.02        31.04         4.01         9.63         8.19         6.61 
TCGA-D7-6528 TCGA-D7-6815 TCGA-D7-6820 TCGA-FP-8099 TCGA-IN-7806 TCGA-IP-7968 
        1.68         3.65         2.93         1.02         6.87         2.53 

$`17P LOSS WILD-TYPE`
TCGA-B7-5816 TCGA-BR-6452 TCGA-BR-6455 TCGA-BR-6457 TCGA-BR-6458 TCGA-BR-6563 
        5.62         0.95         1.41         1.35         1.35         0.85 
TCGA-BR-6564 TCGA-BR-6565 TCGA-BR-6566 TCGA-BR-6705 TCGA-BR-6706 TCGA-BR-6707 
        0.82         0.62         0.62         1.71         2.17         0.99 
TCGA-BR-6709 TCGA-BR-6710 TCGA-BR-6801 TCGA-BR-6802 TCGA-BR-6803 TCGA-BR-6852 
        1.22         0.66         1.12         0.76         0.66         0.26 
TCGA-BR-7196 TCGA-BR-7703 TCGA-BR-7704 TCGA-BR-7707 TCGA-BR-7716 TCGA-BR-7717 
        1.22         0.46         1.25         0.13         0.82         0.69 
TCGA-BR-7722 TCGA-BR-7723 TCGA-BR-7851 TCGA-BR-7901 TCGA-BR-7957 TCGA-BR-7958 
        0.16         4.54         0.99         0.95         0.69         0.16 
TCGA-BR-8059 TCGA-BR-8060 TCGA-BR-8077 TCGA-BR-8078 TCGA-BR-8080 TCGA-BR-8081 
        0.82         1.32         0.69         0.95         0.49         0.46 
TCGA-BR-8284 TCGA-BR-8285 TCGA-BR-8286 TCGA-BR-8291 TCGA-BR-8295 TCGA-BR-8297 
        0.72         0.26         0.43         1.18         1.55         0.76 
TCGA-BR-8592 TCGA-BR-A4IU TCGA-BR-A4IV TCGA-BR-A4IY TCGA-BR-A4IZ TCGA-BR-A4J2 
        0.20         0.59         0.92         0.39         0.79         0.79 
TCGA-BR-A4J4 TCGA-BR-A4J5 TCGA-BR-A4J6 TCGA-BR-A4J8 TCGA-BR-A4J9 TCGA-BR-A4PF 
        0.53         0.43         0.13         0.23         0.10         0.72 
TCGA-BR-A4QI TCGA-BR-A4QL TCGA-CD-5798 TCGA-CD-5800 TCGA-CD-5801 TCGA-CD-5802 
        0.49         2.24         0.82         0.36         0.49         0.30 
TCGA-CD-5803 TCGA-CG-4305 TCGA-CG-4306 TCGA-CG-4436 TCGA-CG-4441 TCGA-CG-4444 
        0.07        15.95         1.02        52.96        14.01        47.05 
TCGA-CG-4449 TCGA-CG-4455 TCGA-CG-4460 TCGA-CG-4462 TCGA-CG-4465 TCGA-CG-4466 
       19.07        12.03        21.99         1.02         8.98        18.94 
TCGA-CG-4472 TCGA-CG-4474 TCGA-CG-5716 TCGA-CG-5717 TCGA-CG-5718 TCGA-CG-5720 
       12.00         1.02         1.02         6.94         1.02         0.99 
TCGA-CG-5721 TCGA-CG-5722 TCGA-CG-5723 TCGA-CG-5724 TCGA-CG-5726 TCGA-CG-5728 
        5.98         0.95        70.06        12.03        28.96        65.10 
TCGA-CG-5732 TCGA-CG-5733 TCGA-CG-5734 TCGA-D7-5577 TCGA-D7-5578 TCGA-D7-5579 
       55.04        21.07         7.99         8.65         3.58         4.54 
TCGA-D7-6518 TCGA-D7-6519 TCGA-D7-6522 TCGA-D7-6524 TCGA-D7-6525 TCGA-D7-6527 
        9.80        15.65         6.90         0.69         5.95         4.14 
TCGA-D7-6817 TCGA-D7-6818 TCGA-D7-6822 TCGA-EQ-5647 TCGA-EQ-8122 TCGA-F1-6177 
        4.70         4.04         4.27         0.62         7.79         6.54 
TCGA-F1-6874 TCGA-F1-6875 TCGA-FP-7735 TCGA-FP-7829 TCGA-FP-7916 TCGA-FP-7998 
        2.01        72.23         0.39         0.20         3.02         3.58 
TCGA-FP-8209 TCGA-FP-8210 TCGA-FP-8631 TCGA-HJ-7597 TCGA-IN-7808 
       59.05         5.03         0.56        26.43         3.55 

      17P LOSS CNV 17P LOSS WILD-TYPE 
              0.10               0.07 
      17P LOSS CNV 17P LOSS WILD-TYPE 
             54.05              72.23 
      17P LOSS CNV 17P LOSS WILD-TYPE 
             3.335              1.020 
[1] "0.1 - 54.0 (3.3)" "0.1 - 72.2 (1.0)"
        TCGA-B7-5816         TCGA-B7-5818         TCGA-BR-6452 
"17P LOSS WILD-TYPE"       "17P LOSS CNV" "17P LOSS WILD-TYPE" 
        TCGA-BR-6455         TCGA-BR-6457         TCGA-BR-6458 
"17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" 
        TCGA-BR-6563         TCGA-BR-6564         TCGA-BR-6565 
"17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" 
        TCGA-BR-6566         TCGA-BR-6705         TCGA-BR-6706 
"17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" 
        TCGA-BR-6707         TCGA-BR-6709         TCGA-BR-6710 
"17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" 
        TCGA-BR-6801         TCGA-BR-6802         TCGA-BR-6803 
"17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" 
        TCGA-BR-6852         TCGA-BR-7196         TCGA-BR-7197 
"17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE"       "17P LOSS CNV" 
        TCGA-BR-7703         TCGA-BR-7704         TCGA-BR-7707 
"17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" 
        TCGA-BR-7715         TCGA-BR-7716         TCGA-BR-7717 
      "17P LOSS CNV" "17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" 
        TCGA-BR-7722         TCGA-BR-7723         TCGA-BR-7851 
"17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" 
        TCGA-BR-7901         TCGA-BR-7957         TCGA-BR-7958 
"17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" 
        TCGA-BR-7959         TCGA-BR-8059         TCGA-BR-8060 
      "17P LOSS CNV" "17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" 
        TCGA-BR-8077         TCGA-BR-8078         TCGA-BR-8080 
"17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" 
        TCGA-BR-8081         TCGA-BR-8284         TCGA-BR-8285 
"17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" 
        TCGA-BR-8286         TCGA-BR-8289         TCGA-BR-8291 
"17P LOSS WILD-TYPE"       "17P LOSS CNV" "17P LOSS WILD-TYPE" 
        TCGA-BR-8295         TCGA-BR-8296         TCGA-BR-8297 
"17P LOSS WILD-TYPE"       "17P LOSS CNV" "17P LOSS WILD-TYPE" 
        TCGA-BR-8592         TCGA-BR-A4IU         TCGA-BR-A4IV 
"17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" 
        TCGA-BR-A4IY         TCGA-BR-A4IZ         TCGA-BR-A4J1 
"17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE"       "17P LOSS CNV" 
        TCGA-BR-A4J2         TCGA-BR-A4J4         TCGA-BR-A4J5 
"17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" 
        TCGA-BR-A4J6         TCGA-BR-A4J8         TCGA-BR-A4J9 
"17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" 
        TCGA-BR-A4PF         TCGA-BR-A4QI         TCGA-BR-A4QL 
"17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" 
        TCGA-CD-5798         TCGA-CD-5799         TCGA-CD-5800 
"17P LOSS WILD-TYPE"       "17P LOSS CNV" "17P LOSS WILD-TYPE" 
        TCGA-CD-5801         TCGA-CD-5802         TCGA-CD-5803 
"17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" 
        TCGA-CG-4300         TCGA-CG-4301         TCGA-CG-4304 
      "17P LOSS CNV"       "17P LOSS CNV"       "17P LOSS CNV" 
        TCGA-CG-4305         TCGA-CG-4306         TCGA-CG-4436 
"17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" 
        TCGA-CG-4437         TCGA-CG-4438         TCGA-CG-4440 
      "17P LOSS CNV"       "17P LOSS CNV"       "17P LOSS CNV" 
        TCGA-CG-4441         TCGA-CG-4443         TCGA-CG-4444 
"17P LOSS WILD-TYPE"       "17P LOSS CNV" "17P LOSS WILD-TYPE" 
        TCGA-CG-4449         TCGA-CG-4455         TCGA-CG-4460 
"17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" 
        TCGA-CG-4462         TCGA-CG-4465         TCGA-CG-4466 
"17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" 
        TCGA-CG-4469         TCGA-CG-4472         TCGA-CG-4474 
      "17P LOSS CNV" "17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" 
        TCGA-CG-4477         TCGA-CG-5716         TCGA-CG-5717 
      "17P LOSS CNV" "17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" 
        TCGA-CG-5718         TCGA-CG-5719         TCGA-CG-5720 
"17P LOSS WILD-TYPE"       "17P LOSS CNV" "17P LOSS WILD-TYPE" 
        TCGA-CG-5721         TCGA-CG-5722         TCGA-CG-5723 
"17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" 
        TCGA-CG-5724         TCGA-CG-5725         TCGA-CG-5726 
"17P LOSS WILD-TYPE"       "17P LOSS CNV" "17P LOSS WILD-TYPE" 
        TCGA-CG-5727         TCGA-CG-5728         TCGA-CG-5730 
      "17P LOSS CNV" "17P LOSS WILD-TYPE"       "17P LOSS CNV" 
        TCGA-CG-5732         TCGA-CG-5733         TCGA-CG-5734 
"17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" 
        TCGA-D7-5577         TCGA-D7-5578         TCGA-D7-5579 
"17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" 
        TCGA-D7-6518         TCGA-D7-6519         TCGA-D7-6520 
"17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE"       "17P LOSS CNV" 
        TCGA-D7-6521         TCGA-D7-6522         TCGA-D7-6524 
      "17P LOSS CNV" "17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" 
        TCGA-D7-6525         TCGA-D7-6526         TCGA-D7-6527 
"17P LOSS WILD-TYPE"       "17P LOSS CNV" "17P LOSS WILD-TYPE" 
        TCGA-D7-6528         TCGA-D7-6815         TCGA-D7-6817 
      "17P LOSS CNV"       "17P LOSS CNV" "17P LOSS WILD-TYPE" 
        TCGA-D7-6818         TCGA-D7-6820         TCGA-D7-6822 
"17P LOSS WILD-TYPE"       "17P LOSS CNV" "17P LOSS WILD-TYPE" 
        TCGA-EQ-5647         TCGA-EQ-8122         TCGA-F1-6177 
"17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" 
        TCGA-F1-6874         TCGA-F1-6875         TCGA-FP-7735 
"17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" 
        TCGA-FP-7829         TCGA-FP-7916         TCGA-FP-7998 
"17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" 
        TCGA-FP-8099         TCGA-FP-8209         TCGA-FP-8210 
      "17P LOSS CNV" "17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" 
        TCGA-FP-8631         TCGA-HJ-7597         TCGA-IN-7806 
"17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE"       "17P LOSS CNV" 
        TCGA-IN-7808         TCGA-IP-7968 
"17P LOSS WILD-TYPE"       "17P LOSS CNV" 
        TCGA-B7-5816         TCGA-B7-5818         TCGA-BR-6452 
"17P LOSS WILD-TYPE"       "17P LOSS CNV" "17P LOSS WILD-TYPE" 
        TCGA-BR-6455         TCGA-BR-6457         TCGA-BR-6458 
"17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" 
        TCGA-BR-6563         TCGA-BR-6564         TCGA-BR-6565 
"17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" 
        TCGA-BR-6566         TCGA-BR-6705         TCGA-BR-6706 
"17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" 
        TCGA-BR-6707         TCGA-BR-6709         TCGA-BR-6710 
"17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" 
        TCGA-BR-6801         TCGA-BR-6802         TCGA-BR-6803 
"17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" 
        TCGA-BR-6852         TCGA-BR-7196         TCGA-BR-7197 
"17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE"       "17P LOSS CNV" 
        TCGA-BR-7703         TCGA-BR-7704         TCGA-BR-7707 
"17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" 
        TCGA-BR-7715         TCGA-BR-7716         TCGA-BR-7717 
      "17P LOSS CNV" "17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" 
        TCGA-BR-7722         TCGA-BR-7723         TCGA-BR-7851 
"17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" 
        TCGA-BR-7901         TCGA-BR-7957         TCGA-BR-7958 
"17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" 
        TCGA-BR-7959         TCGA-BR-8059         TCGA-BR-8060 
      "17P LOSS CNV" "17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" 
        TCGA-BR-8077         TCGA-BR-8078         TCGA-BR-8080 
"17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" 
        TCGA-BR-8081         TCGA-BR-8284         TCGA-BR-8285 
"17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" 
        TCGA-BR-8286         TCGA-BR-8289         TCGA-BR-8291 
"17P LOSS WILD-TYPE"       "17P LOSS CNV" "17P LOSS WILD-TYPE" 
        TCGA-BR-8295         TCGA-BR-8296         TCGA-BR-8297 
"17P LOSS WILD-TYPE"       "17P LOSS CNV" "17P LOSS WILD-TYPE" 
        TCGA-BR-8592         TCGA-BR-A4IU         TCGA-BR-A4IV 
"17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" 
        TCGA-BR-A4IY         TCGA-BR-A4IZ         TCGA-BR-A4J1 
"17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE"       "17P LOSS CNV" 
        TCGA-BR-A4J2         TCGA-BR-A4J4         TCGA-BR-A4J5 
"17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" 
        TCGA-BR-A4J6         TCGA-BR-A4J8         TCGA-BR-A4J9 
"17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" 
        TCGA-BR-A4PF         TCGA-BR-A4QI         TCGA-BR-A4QL 
"17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" 
        TCGA-CD-5798         TCGA-CD-5799         TCGA-CD-5800 
"17P LOSS WILD-TYPE"       "17P LOSS CNV" "17P LOSS WILD-TYPE" 
        TCGA-CD-5801         TCGA-CD-5802         TCGA-CD-5803 
"17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" 
        TCGA-CG-4300         TCGA-CG-4301         TCGA-CG-4304 
      "17P LOSS CNV"       "17P LOSS CNV"       "17P LOSS CNV" 
        TCGA-CG-4305         TCGA-CG-4306         TCGA-CG-4436 
"17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" 
        TCGA-CG-4437         TCGA-CG-4438         TCGA-CG-4440 
      "17P LOSS CNV"       "17P LOSS CNV"       "17P LOSS CNV" 
        TCGA-CG-4441         TCGA-CG-4443         TCGA-CG-4444 
"17P LOSS WILD-TYPE"       "17P LOSS CNV" "17P LOSS WILD-TYPE" 
        TCGA-CG-4449         TCGA-CG-4455         TCGA-CG-4460 
"17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" 
        TCGA-CG-4462         TCGA-CG-4465         TCGA-CG-4466 
"17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" 
        TCGA-CG-4469         TCGA-CG-4472         TCGA-CG-4474 
      "17P LOSS CNV" "17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" 
        TCGA-CG-4477         TCGA-CG-5716         TCGA-CG-5717 
      "17P LOSS CNV" "17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" 
        TCGA-CG-5718         TCGA-CG-5719         TCGA-CG-5720 
"17P LOSS WILD-TYPE"       "17P LOSS CNV" "17P LOSS WILD-TYPE" 
        TCGA-CG-5721         TCGA-CG-5722         TCGA-CG-5723 
"17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" 
        TCGA-CG-5724         TCGA-CG-5725         TCGA-CG-5726 
"17P LOSS WILD-TYPE"       "17P LOSS CNV" "17P LOSS WILD-TYPE" 
        TCGA-CG-5727         TCGA-CG-5728         TCGA-CG-5730 
      "17P LOSS CNV" "17P LOSS WILD-TYPE"       "17P LOSS CNV" 
        TCGA-CG-5732         TCGA-CG-5733         TCGA-CG-5734 
"17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" 
        TCGA-D7-5577         TCGA-D7-5578         TCGA-D7-5579 
"17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" 
        TCGA-D7-6518         TCGA-D7-6519         TCGA-D7-6520 
"17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE"       "17P LOSS CNV" 
        TCGA-D7-6521         TCGA-D7-6522         TCGA-D7-6524 
      "17P LOSS CNV" "17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" 
        TCGA-D7-6525         TCGA-D7-6526         TCGA-D7-6527 
"17P LOSS WILD-TYPE"       "17P LOSS CNV" "17P LOSS WILD-TYPE" 
        TCGA-D7-6528         TCGA-D7-6815         TCGA-D7-6817 
      "17P LOSS CNV"       "17P LOSS CNV" "17P LOSS WILD-TYPE" 
        TCGA-D7-6818         TCGA-D7-6820         TCGA-D7-6822 
"17P LOSS WILD-TYPE"       "17P LOSS CNV" "17P LOSS WILD-TYPE" 
        TCGA-EQ-5647         TCGA-EQ-8122         TCGA-F1-6177 
"17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" 
        TCGA-F1-6874         TCGA-F1-6875         TCGA-FP-7735 
"17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" 
        TCGA-FP-7829         TCGA-FP-7916         TCGA-FP-7998 
"17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" 
        TCGA-FP-8099         TCGA-FP-8209         TCGA-FP-8210 
      "17P LOSS CNV" "17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" 
        TCGA-FP-8631         TCGA-HJ-7597         TCGA-IN-7806 
"17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE"       "17P LOSS CNV" 
        TCGA-IN-7808         TCGA-IP-7968 
"17P LOSS WILD-TYPE"       "17P LOSS CNV" 
        TCGA-B7-5816         TCGA-B7-5818         TCGA-BR-6452 
"17P LOSS WILD-TYPE"       "17P LOSS CNV" "17P LOSS WILD-TYPE" 
        TCGA-BR-6455         TCGA-BR-6457         TCGA-BR-6458 
"17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" 
        TCGA-BR-6563         TCGA-BR-6564         TCGA-BR-6565 
"17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" 
        TCGA-BR-6566         TCGA-BR-6705         TCGA-BR-6706 
"17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" 
        TCGA-BR-6707         TCGA-BR-6709         TCGA-BR-6710 
"17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" 
        TCGA-BR-6801         TCGA-BR-6802         TCGA-BR-6803 
"17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" 
        TCGA-BR-6852         TCGA-BR-7196         TCGA-BR-7197 
"17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE"       "17P LOSS CNV" 
        TCGA-BR-7703         TCGA-BR-7704         TCGA-BR-7707 
"17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" 
        TCGA-BR-7715         TCGA-BR-7716         TCGA-BR-7717 
      "17P LOSS CNV" "17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" 
        TCGA-BR-7722         TCGA-BR-7723         TCGA-BR-7851 
"17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" 
        TCGA-BR-7901         TCGA-BR-7957         TCGA-BR-7958 
"17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" 
        TCGA-BR-7959         TCGA-BR-8059         TCGA-BR-8060 
      "17P LOSS CNV" "17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" 
        TCGA-BR-8077         TCGA-BR-8078         TCGA-BR-8080 
"17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" 
        TCGA-BR-8081         TCGA-BR-8284         TCGA-BR-8285 
"17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" 
        TCGA-BR-8286         TCGA-BR-8289         TCGA-BR-8291 
"17P LOSS WILD-TYPE"       "17P LOSS CNV" "17P LOSS WILD-TYPE" 
        TCGA-BR-8295         TCGA-BR-8296         TCGA-BR-8297 
"17P LOSS WILD-TYPE"       "17P LOSS CNV" "17P LOSS WILD-TYPE" 
        TCGA-BR-8592         TCGA-BR-A4IU         TCGA-BR-A4IV 
"17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" 
        TCGA-BR-A4IY         TCGA-BR-A4IZ         TCGA-BR-A4J1 
"17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE"       "17P LOSS CNV" 
        TCGA-BR-A4J2         TCGA-BR-A4J4         TCGA-BR-A4J5 
"17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" 
        TCGA-BR-A4J6         TCGA-BR-A4J8         TCGA-BR-A4J9 
"17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" 
        TCGA-BR-A4PF         TCGA-BR-A4QI         TCGA-BR-A4QL 
"17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" 
        TCGA-CD-5798         TCGA-CD-5799         TCGA-CD-5800 
"17P LOSS WILD-TYPE"       "17P LOSS CNV" "17P LOSS WILD-TYPE" 
        TCGA-CD-5801         TCGA-CD-5802         TCGA-CD-5803 
"17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" 
        TCGA-CG-4300         TCGA-CG-4301         TCGA-CG-4304 
      "17P LOSS CNV"       "17P LOSS CNV"       "17P LOSS CNV" 
        TCGA-CG-4305         TCGA-CG-4306         TCGA-CG-4436 
"17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" 
        TCGA-CG-4437         TCGA-CG-4438         TCGA-CG-4440 
      "17P LOSS CNV"       "17P LOSS CNV"       "17P LOSS CNV" 
        TCGA-CG-4441         TCGA-CG-4443         TCGA-CG-4444 
"17P LOSS WILD-TYPE"       "17P LOSS CNV" "17P LOSS WILD-TYPE" 
        TCGA-CG-4449         TCGA-CG-4455         TCGA-CG-4460 
"17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" 
        TCGA-CG-4462         TCGA-CG-4465         TCGA-CG-4466 
"17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" 
        TCGA-CG-4469         TCGA-CG-4472         TCGA-CG-4474 
      "17P LOSS CNV" "17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" 
        TCGA-CG-4477         TCGA-CG-5716         TCGA-CG-5717 
      "17P LOSS CNV" "17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" 
        TCGA-CG-5718         TCGA-CG-5719         TCGA-CG-5720 
"17P LOSS WILD-TYPE"       "17P LOSS CNV" "17P LOSS WILD-TYPE" 
        TCGA-CG-5721         TCGA-CG-5722         TCGA-CG-5723 
"17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" 
        TCGA-CG-5724         TCGA-CG-5725         TCGA-CG-5726 
"17P LOSS WILD-TYPE"       "17P LOSS CNV" "17P LOSS WILD-TYPE" 
        TCGA-CG-5727         TCGA-CG-5728         TCGA-CG-5730 
      "17P LOSS CNV" "17P LOSS WILD-TYPE"       "17P LOSS CNV" 
        TCGA-CG-5732         TCGA-CG-5733         TCGA-CG-5734 
"17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" 
        TCGA-D7-5577         TCGA-D7-5578         TCGA-D7-5579 
"17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" 
        TCGA-D7-6518         TCGA-D7-6519         TCGA-D7-6520 
"17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE"       "17P LOSS CNV" 
        TCGA-D7-6521         TCGA-D7-6522         TCGA-D7-6524 
      "17P LOSS CNV" "17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" 
        TCGA-D7-6525         TCGA-D7-6526         TCGA-D7-6527 
"17P LOSS WILD-TYPE"       "17P LOSS CNV" "17P LOSS WILD-TYPE" 
        TCGA-D7-6528         TCGA-D7-6815         TCGA-D7-6817 
      "17P LOSS CNV"       "17P LOSS CNV" "17P LOSS WILD-TYPE" 
        TCGA-D7-6818         TCGA-D7-6820         TCGA-D7-6822 
"17P LOSS WILD-TYPE"       "17P LOSS CNV" "17P LOSS WILD-TYPE" 
        TCGA-EQ-5647         TCGA-EQ-8122         TCGA-F1-6177 
"17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" 
        TCGA-F1-6874         TCGA-F1-6875         TCGA-FP-7735 
"17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" 
        TCGA-FP-7829         TCGA-FP-7916         TCGA-FP-7998 
"17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" 
        TCGA-FP-8099         TCGA-FP-8209         TCGA-FP-8210 
      "17P LOSS CNV" "17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" 
        TCGA-FP-8631         TCGA-HJ-7597         TCGA-IN-7806 
"17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE"       "17P LOSS CNV" 
        TCGA-IN-7808         TCGA-IP-7968 
"17P LOSS WILD-TYPE"       "17P LOSS CNV" 
[1] "hr=" "1.2"
D65V2, continuous
D65V3, binary
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  17P LOSS CNV         11   25
  17P LOSS WILD-TYPE   61   83
        clus
vv       17P LOSS CNV 17P LOSS WILD-TYPE
  FEMALE           11                 61
  MALE             25                 83
                    vv
clus                 STOMACH  ADENOCARCINOMA  DIFFUSE TYPE
  17P LOSS CNV                                           0
  17P LOSS WILD-TYPE                                    10
                    vv
clus                 STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  17P LOSS CNV                                                            2
  17P LOSS WILD-TYPE                                                     14
                    vv
clus                 STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  17P LOSS CNV                                                                       2
  17P LOSS WILD-TYPE                                                                 6
                    vv
clus                 STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE
  17P LOSS CNV                                                              1
  17P LOSS WILD-TYPE                                                        2
                    vv
clus                 STOMACH ADENOCARCINOMA  SIGNET RING TYPE
  17P LOSS CNV                                              0
  17P LOSS WILD-TYPE                                        1
                    vv
clus                 STOMACH ADENOCARCINOMA - DIFFUSE TYPE
  17P LOSS CNV                                           3
  17P LOSS WILD-TYPE                                    13
                    vv
clus                 STOMACH ADENOCARCINOMA - NOT OTHERWISE SPECIFIED (NOS)
  17P LOSS CNV                                                           10
  17P LOSS WILD-TYPE                                                     63
                    vv
clus                 STOMACH INTESTINAL ADENOCARCINOMA - MUCINOUS TYPE
  17P LOSS CNV                                                       2
  17P LOSS WILD-TYPE                                                 5
                    vv
clus                 STOMACH INTESTINAL ADENOCARCINOMA - PAPILLARY TYPE
  17P LOSS CNV                                                        0
  17P LOSS WILD-TYPE                                                  3
                    vv
clus                 STOMACH INTESTINAL ADENOCARCINOMA - TUBULAR TYPE
  17P LOSS CNV                                                      6
  17P LOSS WILD-TYPE                                                4
                    vv
clus                 STOMACH INTESTINAL ADENOCARCINOMA - TYPE NOT OTHERWISE SPECIFIED (NOS)
  17P LOSS CNV                                                                           10
  17P LOSS WILD-TYPE                                                                     18
D65V4, multiclass
                    vv
clus                 T1 T2 T3 T4
  17P LOSS CNV        1 17 10  3
  17P LOSS WILD-TYPE  5 35 46 15
D65V5, multiclass
    clus
vv   17P LOSS CNV 17P LOSS WILD-TYPE
  T1            1                  5
  T2           17                 35
  T3           10                 46
  T4            3                 15
                    vv
clus                 N0 N1 N2 N3
  17P LOSS CNV       12  8  7  3
  17P LOSS WILD-TYPE 32 41 16 12
D65V6, multiclass
    clus
vv   17P LOSS CNV 17P LOSS WILD-TYPE
  N0           12                 32
  N1            8                 41
  N2            7                 16
  N3            3                 12
                    vv
clus                 M0 M1 MX
  17P LOSS CNV       25  4  2
  17P LOSS WILD-TYPE 93 12  6
D65V7, multiclass
    clus
vv   17P LOSS CNV 17P LOSS WILD-TYPE
  M0           25                 93
  M1            4                 12
  MX            2                  6
                    vv
clus                  I II III IV
  17P LOSS CNV        8  7   8  7
  17P LOSS WILD-TYPE 16 30  31 19
D65V8, multiclass
     clus
vv    17P LOSS CNV 17P LOSS WILD-TYPE
  I              8                 16
  II             7                 30
  III            8                 31
  IV             7                 19
D65V9, binary
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  17P LOSS CNV          3   33
  17P LOSS WILD-TYPE    2  142
     clus
vv    17P LOSS CNV 17P LOSS WILD-TYPE
  NO             3                  2
  YES           33                142
                    vv
clus                 R0 R1 R2 RX
  17P LOSS CNV       26  3  3  2
  17P LOSS WILD-TYPE 99  4  9 23
D65V10, multiclass
    clus
vv   17P LOSS CNV 17P LOSS WILD-TYPE
  R0           26                 99
  R1            3                  4
  R2            3                  9
  RX            2                 23
D65V11, continuous

Clustering(66) Variable = 17q loss
D66V1, survival
                    sevent
clus2                  0   1
  17Q LOSS CNV         7   2
  17Q LOSS WILD-TYPE 117  17
      17Q LOSS CNV 17Q LOSS WILD-TYPE 
                 9                134 
      17Q LOSS CNV 17Q LOSS WILD-TYPE 
                 2                 17 
$`17Q LOSS CNV`
TCGA-BR-7959 TCGA-BR-A4J1 TCGA-CG-4300 TCGA-CG-4301 TCGA-CG-4438 TCGA-CG-4440 
        1.08         0.72        20.02         3.02        54.05         4.01 
TCGA-CG-4477 TCGA-D7-6526 TCGA-D7-6820 
        1.02         6.61         2.93 

$`17Q LOSS WILD-TYPE`
TCGA-B7-5816 TCGA-B7-5818 TCGA-BR-6452 TCGA-BR-6455 TCGA-BR-6457 TCGA-BR-6458 
        5.62         0.10         0.95         1.41         1.35         1.35 
TCGA-BR-6563 TCGA-BR-6564 TCGA-BR-6565 TCGA-BR-6566 TCGA-BR-6705 TCGA-BR-6706 
        0.85         0.82         0.62         0.62         1.71         2.17 
TCGA-BR-6707 TCGA-BR-6709 TCGA-BR-6710 TCGA-BR-6801 TCGA-BR-6802 TCGA-BR-6803 
        0.99         1.22         0.66         1.12         0.76         0.66 
TCGA-BR-6852 TCGA-BR-7196 TCGA-BR-7197 TCGA-BR-7703 TCGA-BR-7704 TCGA-BR-7707 
        0.26         1.22         1.48         0.46         1.25         0.13 
TCGA-BR-7715 TCGA-BR-7716 TCGA-BR-7717 TCGA-BR-7722 TCGA-BR-7723 TCGA-BR-7851 
        1.05         0.82         0.69         0.16         4.54         0.99 
TCGA-BR-7901 TCGA-BR-7957 TCGA-BR-7958 TCGA-BR-8059 TCGA-BR-8060 TCGA-BR-8077 
        0.95         0.69         0.16         0.82         1.32         0.69 
TCGA-BR-8078 TCGA-BR-8080 TCGA-BR-8081 TCGA-BR-8284 TCGA-BR-8285 TCGA-BR-8286 
        0.95         0.49         0.46         0.72         0.26         0.43 
TCGA-BR-8289 TCGA-BR-8291 TCGA-BR-8295 TCGA-BR-8296 TCGA-BR-8297 TCGA-BR-8592 
        0.26         1.18         1.55         1.48         0.76         0.20 
TCGA-BR-A4IU TCGA-BR-A4IV TCGA-BR-A4IY TCGA-BR-A4IZ TCGA-BR-A4J2 TCGA-BR-A4J4 
        0.59         0.92         0.39         0.79         0.79         0.53 
TCGA-BR-A4J5 TCGA-BR-A4J6 TCGA-BR-A4J8 TCGA-BR-A4J9 TCGA-BR-A4PF TCGA-BR-A4QI 
        0.43         0.13         0.23         0.10         0.72         0.49 
TCGA-BR-A4QL TCGA-CD-5798 TCGA-CD-5799 TCGA-CD-5800 TCGA-CD-5801 TCGA-CD-5802 
        2.24         0.82         0.69         0.36         0.49         0.30 
TCGA-CD-5803 TCGA-CG-4304 TCGA-CG-4305 TCGA-CG-4306 TCGA-CG-4436 TCGA-CG-4437 
        0.07        27.02        15.95         1.02        52.96         8.05 
TCGA-CG-4441 TCGA-CG-4443 TCGA-CG-4444 TCGA-CG-4449 TCGA-CG-4455 TCGA-CG-4460 
       14.01        29.98        47.05        19.07        12.03        21.99 
TCGA-CG-4462 TCGA-CG-4465 TCGA-CG-4466 TCGA-CG-4469 TCGA-CG-4472 TCGA-CG-4474 
        1.02         8.98        18.94         7.07        12.00         1.02 
TCGA-CG-5716 TCGA-CG-5717 TCGA-CG-5718 TCGA-CG-5719 TCGA-CG-5720 TCGA-CG-5721 
        1.02         6.94         1.02         1.02         0.99         5.98 
TCGA-CG-5722 TCGA-CG-5723 TCGA-CG-5724 TCGA-CG-5725 TCGA-CG-5726 TCGA-CG-5727 
        0.95        70.06        12.03        15.02        28.96        31.04 
TCGA-CG-5728 TCGA-CG-5730 TCGA-CG-5732 TCGA-CG-5733 TCGA-CG-5734 TCGA-D7-5577 
       65.10         4.01        55.04        21.07         7.99         8.65 
TCGA-D7-5578 TCGA-D7-5579 TCGA-D7-6518 TCGA-D7-6519 TCGA-D7-6520 TCGA-D7-6521 
        3.58         4.54         9.80        15.65         9.63         8.19 
TCGA-D7-6522 TCGA-D7-6524 TCGA-D7-6525 TCGA-D7-6527 TCGA-D7-6528 TCGA-D7-6815 
        6.90         0.69         5.95         4.14         1.68         3.65 
TCGA-D7-6817 TCGA-D7-6818 TCGA-D7-6822 TCGA-EQ-5647 TCGA-EQ-8122 TCGA-F1-6177 
        4.70         4.04         4.27         0.62         7.79         6.54 
TCGA-F1-6874 TCGA-F1-6875 TCGA-FP-7735 TCGA-FP-7829 TCGA-FP-7916 TCGA-FP-7998 
        2.01        72.23         0.39         0.20         3.02         3.58 
TCGA-FP-8099 TCGA-FP-8209 TCGA-FP-8210 TCGA-FP-8631 TCGA-HJ-7597 TCGA-IN-7806 
        1.02        59.05         5.03         0.56        26.43         6.87 
TCGA-IN-7808 TCGA-IP-7968 
        3.55         2.53 

      17Q LOSS CNV 17Q LOSS WILD-TYPE 
              0.72               0.07 
      17Q LOSS CNV 17Q LOSS WILD-TYPE 
             54.05              72.23 
      17Q LOSS CNV 17Q LOSS WILD-TYPE 
              3.02               1.22 
[1] "0.7 - 54.0 (3.0)" "0.1 - 72.2 (1.2)"
        TCGA-B7-5816         TCGA-B7-5818         TCGA-BR-6452 
"17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" 
        TCGA-BR-6455         TCGA-BR-6457         TCGA-BR-6458 
"17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" 
        TCGA-BR-6563         TCGA-BR-6564         TCGA-BR-6565 
"17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" 
        TCGA-BR-6566         TCGA-BR-6705         TCGA-BR-6706 
"17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" 
        TCGA-BR-6707         TCGA-BR-6709         TCGA-BR-6710 
"17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" 
        TCGA-BR-6801         TCGA-BR-6802         TCGA-BR-6803 
"17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" 
        TCGA-BR-6852         TCGA-BR-7196         TCGA-BR-7197 
"17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" 
        TCGA-BR-7703         TCGA-BR-7704         TCGA-BR-7707 
"17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" 
        TCGA-BR-7715         TCGA-BR-7716         TCGA-BR-7717 
"17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" 
        TCGA-BR-7722         TCGA-BR-7723         TCGA-BR-7851 
"17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" 
        TCGA-BR-7901         TCGA-BR-7957         TCGA-BR-7958 
"17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" 
        TCGA-BR-7959         TCGA-BR-8059         TCGA-BR-8060 
      "17Q LOSS CNV" "17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" 
        TCGA-BR-8077         TCGA-BR-8078         TCGA-BR-8080 
"17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" 
        TCGA-BR-8081         TCGA-BR-8284         TCGA-BR-8285 
"17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" 
        TCGA-BR-8286         TCGA-BR-8289         TCGA-BR-8291 
"17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" 
        TCGA-BR-8295         TCGA-BR-8296         TCGA-BR-8297 
"17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" 
        TCGA-BR-8592         TCGA-BR-A4IU         TCGA-BR-A4IV 
"17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" 
        TCGA-BR-A4IY         TCGA-BR-A4IZ         TCGA-BR-A4J1 
"17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE"       "17Q LOSS CNV" 
        TCGA-BR-A4J2         TCGA-BR-A4J4         TCGA-BR-A4J5 
"17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" 
        TCGA-BR-A4J6         TCGA-BR-A4J8         TCGA-BR-A4J9 
"17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" 
        TCGA-BR-A4PF         TCGA-BR-A4QI         TCGA-BR-A4QL 
"17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" 
        TCGA-CD-5798         TCGA-CD-5799         TCGA-CD-5800 
"17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" 
        TCGA-CD-5801         TCGA-CD-5802         TCGA-CD-5803 
"17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" 
        TCGA-CG-4300         TCGA-CG-4301         TCGA-CG-4304 
      "17Q LOSS CNV"       "17Q LOSS CNV" "17Q LOSS WILD-TYPE" 
        TCGA-CG-4305         TCGA-CG-4306         TCGA-CG-4436 
"17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" 
        TCGA-CG-4437         TCGA-CG-4438         TCGA-CG-4440 
"17Q LOSS WILD-TYPE"       "17Q LOSS CNV"       "17Q LOSS CNV" 
        TCGA-CG-4441         TCGA-CG-4443         TCGA-CG-4444 
"17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" 
        TCGA-CG-4449         TCGA-CG-4455         TCGA-CG-4460 
"17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" 
        TCGA-CG-4462         TCGA-CG-4465         TCGA-CG-4466 
"17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" 
        TCGA-CG-4469         TCGA-CG-4472         TCGA-CG-4474 
"17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" 
        TCGA-CG-4477         TCGA-CG-5716         TCGA-CG-5717 
      "17Q LOSS CNV" "17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" 
        TCGA-CG-5718         TCGA-CG-5719         TCGA-CG-5720 
"17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" 
        TCGA-CG-5721         TCGA-CG-5722         TCGA-CG-5723 
"17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" 
        TCGA-CG-5724         TCGA-CG-5725         TCGA-CG-5726 
"17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" 
        TCGA-CG-5727         TCGA-CG-5728         TCGA-CG-5730 
"17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" 
        TCGA-CG-5732         TCGA-CG-5733         TCGA-CG-5734 
"17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" 
        TCGA-D7-5577         TCGA-D7-5578         TCGA-D7-5579 
"17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" 
        TCGA-D7-6518         TCGA-D7-6519         TCGA-D7-6520 
"17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" 
        TCGA-D7-6521         TCGA-D7-6522         TCGA-D7-6524 
"17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" 
        TCGA-D7-6525         TCGA-D7-6526         TCGA-D7-6527 
"17Q LOSS WILD-TYPE"       "17Q LOSS CNV" "17Q LOSS WILD-TYPE" 
        TCGA-D7-6528         TCGA-D7-6815         TCGA-D7-6817 
"17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" 
        TCGA-D7-6818         TCGA-D7-6820         TCGA-D7-6822 
"17Q LOSS WILD-TYPE"       "17Q LOSS CNV" "17Q LOSS WILD-TYPE" 
        TCGA-EQ-5647         TCGA-EQ-8122         TCGA-F1-6177 
"17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" 
        TCGA-F1-6874         TCGA-F1-6875         TCGA-FP-7735 
"17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" 
        TCGA-FP-7829         TCGA-FP-7916         TCGA-FP-7998 
"17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" 
        TCGA-FP-8099         TCGA-FP-8209         TCGA-FP-8210 
"17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" 
        TCGA-FP-8631         TCGA-HJ-7597         TCGA-IN-7806 
"17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" 
        TCGA-IN-7808         TCGA-IP-7968 
"17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" 
        TCGA-B7-5816         TCGA-B7-5818         TCGA-BR-6452 
"17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" 
        TCGA-BR-6455         TCGA-BR-6457         TCGA-BR-6458 
"17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" 
        TCGA-BR-6563         TCGA-BR-6564         TCGA-BR-6565 
"17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" 
        TCGA-BR-6566         TCGA-BR-6705         TCGA-BR-6706 
"17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" 
        TCGA-BR-6707         TCGA-BR-6709         TCGA-BR-6710 
"17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" 
        TCGA-BR-6801         TCGA-BR-6802         TCGA-BR-6803 
"17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" 
        TCGA-BR-6852         TCGA-BR-7196         TCGA-BR-7197 
"17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" 
        TCGA-BR-7703         TCGA-BR-7704         TCGA-BR-7707 
"17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" 
        TCGA-BR-7715         TCGA-BR-7716         TCGA-BR-7717 
"17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" 
        TCGA-BR-7722         TCGA-BR-7723         TCGA-BR-7851 
"17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" 
        TCGA-BR-7901         TCGA-BR-7957         TCGA-BR-7958 
"17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" 
        TCGA-BR-7959         TCGA-BR-8059         TCGA-BR-8060 
      "17Q LOSS CNV" "17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" 
        TCGA-BR-8077         TCGA-BR-8078         TCGA-BR-8080 
"17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" 
        TCGA-BR-8081         TCGA-BR-8284         TCGA-BR-8285 
"17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" 
        TCGA-BR-8286         TCGA-BR-8289         TCGA-BR-8291 
"17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" 
        TCGA-BR-8295         TCGA-BR-8296         TCGA-BR-8297 
"17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" 
        TCGA-BR-8592         TCGA-BR-A4IU         TCGA-BR-A4IV 
"17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" 
        TCGA-BR-A4IY         TCGA-BR-A4IZ         TCGA-BR-A4J1 
"17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE"       "17Q LOSS CNV" 
        TCGA-BR-A4J2         TCGA-BR-A4J4         TCGA-BR-A4J5 
"17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" 
        TCGA-BR-A4J6         TCGA-BR-A4J8         TCGA-BR-A4J9 
"17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" 
        TCGA-BR-A4PF         TCGA-BR-A4QI         TCGA-BR-A4QL 
"17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" 
        TCGA-CD-5798         TCGA-CD-5799         TCGA-CD-5800 
"17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" 
        TCGA-CD-5801         TCGA-CD-5802         TCGA-CD-5803 
"17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" 
        TCGA-CG-4300         TCGA-CG-4301         TCGA-CG-4304 
      "17Q LOSS CNV"       "17Q LOSS CNV" "17Q LOSS WILD-TYPE" 
        TCGA-CG-4305         TCGA-CG-4306         TCGA-CG-4436 
"17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" 
        TCGA-CG-4437         TCGA-CG-4438         TCGA-CG-4440 
"17Q LOSS WILD-TYPE"       "17Q LOSS CNV"       "17Q LOSS CNV" 
        TCGA-CG-4441         TCGA-CG-4443         TCGA-CG-4444 
"17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" 
        TCGA-CG-4449         TCGA-CG-4455         TCGA-CG-4460 
"17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" 
        TCGA-CG-4462         TCGA-CG-4465         TCGA-CG-4466 
"17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" 
        TCGA-CG-4469         TCGA-CG-4472         TCGA-CG-4474 
"17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" 
        TCGA-CG-4477         TCGA-CG-5716         TCGA-CG-5717 
      "17Q LOSS CNV" "17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" 
        TCGA-CG-5718         TCGA-CG-5719         TCGA-CG-5720 
"17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" 
        TCGA-CG-5721         TCGA-CG-5722         TCGA-CG-5723 
"17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" 
        TCGA-CG-5724         TCGA-CG-5725         TCGA-CG-5726 
"17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" 
        TCGA-CG-5727         TCGA-CG-5728         TCGA-CG-5730 
"17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" 
        TCGA-CG-5732         TCGA-CG-5733         TCGA-CG-5734 
"17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" 
        TCGA-D7-5577         TCGA-D7-5578         TCGA-D7-5579 
"17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" 
        TCGA-D7-6518         TCGA-D7-6519         TCGA-D7-6520 
"17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" 
        TCGA-D7-6521         TCGA-D7-6522         TCGA-D7-6524 
"17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" 
        TCGA-D7-6525         TCGA-D7-6526         TCGA-D7-6527 
"17Q LOSS WILD-TYPE"       "17Q LOSS CNV" "17Q LOSS WILD-TYPE" 
        TCGA-D7-6528         TCGA-D7-6815         TCGA-D7-6817 
"17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" 
        TCGA-D7-6818         TCGA-D7-6820         TCGA-D7-6822 
"17Q LOSS WILD-TYPE"       "17Q LOSS CNV" "17Q LOSS WILD-TYPE" 
        TCGA-EQ-5647         TCGA-EQ-8122         TCGA-F1-6177 
"17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" 
        TCGA-F1-6874         TCGA-F1-6875         TCGA-FP-7735 
"17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" 
        TCGA-FP-7829         TCGA-FP-7916         TCGA-FP-7998 
"17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" 
        TCGA-FP-8099         TCGA-FP-8209         TCGA-FP-8210 
"17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" 
        TCGA-FP-8631         TCGA-HJ-7597         TCGA-IN-7806 
"17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" 
        TCGA-IN-7808         TCGA-IP-7968 
"17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" 
        TCGA-B7-5816         TCGA-B7-5818         TCGA-BR-6452 
"17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" 
        TCGA-BR-6455         TCGA-BR-6457         TCGA-BR-6458 
"17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" 
        TCGA-BR-6563         TCGA-BR-6564         TCGA-BR-6565 
"17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" 
        TCGA-BR-6566         TCGA-BR-6705         TCGA-BR-6706 
"17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" 
        TCGA-BR-6707         TCGA-BR-6709         TCGA-BR-6710 
"17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" 
        TCGA-BR-6801         TCGA-BR-6802         TCGA-BR-6803 
"17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" 
        TCGA-BR-6852         TCGA-BR-7196         TCGA-BR-7197 
"17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" 
        TCGA-BR-7703         TCGA-BR-7704         TCGA-BR-7707 
"17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" 
        TCGA-BR-7715         TCGA-BR-7716         TCGA-BR-7717 
"17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" 
        TCGA-BR-7722         TCGA-BR-7723         TCGA-BR-7851 
"17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" 
        TCGA-BR-7901         TCGA-BR-7957         TCGA-BR-7958 
"17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" 
        TCGA-BR-7959         TCGA-BR-8059         TCGA-BR-8060 
      "17Q LOSS CNV" "17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" 
        TCGA-BR-8077         TCGA-BR-8078         TCGA-BR-8080 
"17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" 
        TCGA-BR-8081         TCGA-BR-8284         TCGA-BR-8285 
"17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" 
        TCGA-BR-8286         TCGA-BR-8289         TCGA-BR-8291 
"17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" 
        TCGA-BR-8295         TCGA-BR-8296         TCGA-BR-8297 
"17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" 
        TCGA-BR-8592         TCGA-BR-A4IU         TCGA-BR-A4IV 
"17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" 
        TCGA-BR-A4IY         TCGA-BR-A4IZ         TCGA-BR-A4J1 
"17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE"       "17Q LOSS CNV" 
        TCGA-BR-A4J2         TCGA-BR-A4J4         TCGA-BR-A4J5 
"17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" 
        TCGA-BR-A4J6         TCGA-BR-A4J8         TCGA-BR-A4J9 
"17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" 
        TCGA-BR-A4PF         TCGA-BR-A4QI         TCGA-BR-A4QL 
"17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" 
        TCGA-CD-5798         TCGA-CD-5799         TCGA-CD-5800 
"17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" 
        TCGA-CD-5801         TCGA-CD-5802         TCGA-CD-5803 
"17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" 
        TCGA-CG-4300         TCGA-CG-4301         TCGA-CG-4304 
      "17Q LOSS CNV"       "17Q LOSS CNV" "17Q LOSS WILD-TYPE" 
        TCGA-CG-4305         TCGA-CG-4306         TCGA-CG-4436 
"17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" 
        TCGA-CG-4437         TCGA-CG-4438         TCGA-CG-4440 
"17Q LOSS WILD-TYPE"       "17Q LOSS CNV"       "17Q LOSS CNV" 
        TCGA-CG-4441         TCGA-CG-4443         TCGA-CG-4444 
"17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" 
        TCGA-CG-4449         TCGA-CG-4455         TCGA-CG-4460 
"17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" 
        TCGA-CG-4462         TCGA-CG-4465         TCGA-CG-4466 
"17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" 
        TCGA-CG-4469         TCGA-CG-4472         TCGA-CG-4474 
"17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" 
        TCGA-CG-4477         TCGA-CG-5716         TCGA-CG-5717 
      "17Q LOSS CNV" "17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" 
        TCGA-CG-5718         TCGA-CG-5719         TCGA-CG-5720 
"17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" 
        TCGA-CG-5721         TCGA-CG-5722         TCGA-CG-5723 
"17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" 
        TCGA-CG-5724         TCGA-CG-5725         TCGA-CG-5726 
"17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" 
        TCGA-CG-5727         TCGA-CG-5728         TCGA-CG-5730 
"17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" 
        TCGA-CG-5732         TCGA-CG-5733         TCGA-CG-5734 
"17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" 
        TCGA-D7-5577         TCGA-D7-5578         TCGA-D7-5579 
"17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" 
        TCGA-D7-6518         TCGA-D7-6519         TCGA-D7-6520 
"17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" 
        TCGA-D7-6521         TCGA-D7-6522         TCGA-D7-6524 
"17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" 
        TCGA-D7-6525         TCGA-D7-6526         TCGA-D7-6527 
"17Q LOSS WILD-TYPE"       "17Q LOSS CNV" "17Q LOSS WILD-TYPE" 
        TCGA-D7-6528         TCGA-D7-6815         TCGA-D7-6817 
"17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" 
        TCGA-D7-6818         TCGA-D7-6820         TCGA-D7-6822 
"17Q LOSS WILD-TYPE"       "17Q LOSS CNV" "17Q LOSS WILD-TYPE" 
        TCGA-EQ-5647         TCGA-EQ-8122         TCGA-F1-6177 
"17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" 
        TCGA-F1-6874         TCGA-F1-6875         TCGA-FP-7735 
"17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" 
        TCGA-FP-7829         TCGA-FP-7916         TCGA-FP-7998 
"17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" 
        TCGA-FP-8099         TCGA-FP-8209         TCGA-FP-8210 
"17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" 
        TCGA-FP-8631         TCGA-HJ-7597         TCGA-IN-7806 
"17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" 
        TCGA-IN-7808         TCGA-IP-7968 
"17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" 
[1] "hr=" "1.6"
D66V2, continuous
D66V3, binary
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  17Q LOSS CNV          5    6
  17Q LOSS WILD-TYPE   67  102
        clus
vv       17Q LOSS CNV 17Q LOSS WILD-TYPE
  FEMALE            5                 67
  MALE              6                102
                    vv
clus                 STOMACH  ADENOCARCINOMA  DIFFUSE TYPE
  17Q LOSS CNV                                           0
  17Q LOSS WILD-TYPE                                    10
                    vv
clus                 STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  17Q LOSS CNV                                                            1
  17Q LOSS WILD-TYPE                                                     15
                    vv
clus                 STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  17Q LOSS CNV                                                                       0
  17Q LOSS WILD-TYPE                                                                 8
                    vv
clus                 STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE
  17Q LOSS CNV                                                              1
  17Q LOSS WILD-TYPE                                                        2
                    vv
clus                 STOMACH ADENOCARCINOMA  SIGNET RING TYPE
  17Q LOSS CNV                                              0
  17Q LOSS WILD-TYPE                                        1
                    vv
clus                 STOMACH ADENOCARCINOMA - DIFFUSE TYPE
  17Q LOSS CNV                                           0
  17Q LOSS WILD-TYPE                                    16
                    vv
clus                 STOMACH ADENOCARCINOMA - NOT OTHERWISE SPECIFIED (NOS)
  17Q LOSS CNV                                                            3
  17Q LOSS WILD-TYPE                                                     70
                    vv
clus                 STOMACH INTESTINAL ADENOCARCINOMA - MUCINOUS TYPE
  17Q LOSS CNV                                                       0
  17Q LOSS WILD-TYPE                                                 7
                    vv
clus                 STOMACH INTESTINAL ADENOCARCINOMA - PAPILLARY TYPE
  17Q LOSS CNV                                                        0
  17Q LOSS WILD-TYPE                                                  3
                    vv
clus                 STOMACH INTESTINAL ADENOCARCINOMA - TUBULAR TYPE
  17Q LOSS CNV                                                      3
  17Q LOSS WILD-TYPE                                                7
                    vv
clus                 STOMACH INTESTINAL ADENOCARCINOMA - TYPE NOT OTHERWISE SPECIFIED (NOS)
  17Q LOSS CNV                                                                            3
  17Q LOSS WILD-TYPE                                                                     25
D66V4, multiclass
                    vv
clus                 T1 T2 T3 T4
  17Q LOSS CNV        0  4  3  2
  17Q LOSS WILD-TYPE  6 48 53 16
D66V5, multiclass
    clus
vv   17Q LOSS CNV 17Q LOSS WILD-TYPE
  T1            0                  6
  T2            4                 48
  T3            3                 53
  T4            2                 16
                    vv
clus                 N0 N1 N2 N3
  17Q LOSS CNV        2  2  3  1
  17Q LOSS WILD-TYPE 42 47 20 14
D66V6, multiclass
    clus
vv   17Q LOSS CNV 17Q LOSS WILD-TYPE
  N0            2                 42
  N1            2                 47
  N2            3                 20
  N3            1                 14
                    vv
clus                  M0  M1  MX
  17Q LOSS CNV         6   2   1
  17Q LOSS WILD-TYPE 112  14   7
D66V7, multiclass
    clus
vv   17Q LOSS CNV 17Q LOSS WILD-TYPE
  M0            6                112
  M1            2                 14
  MX            1                  7
                    vv
clus                  I II III IV
  17Q LOSS CNV        2  1   2  3
  17Q LOSS WILD-TYPE 22 36  37 23
D66V8, multiclass
     clus
vv    17Q LOSS CNV 17Q LOSS WILD-TYPE
  I              2                 22
  II             1                 36
  III            2                 37
  IV             3                 23
D66V9, binary
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  17Q LOSS CNV          1   10
  17Q LOSS WILD-TYPE    4  165
     clus
vv    17Q LOSS CNV 17Q LOSS WILD-TYPE
  NO             1                  4
  YES           10                165
                    vv
clus                  R0  R1  R2  RX
  17Q LOSS CNV         8   0   2   1
  17Q LOSS WILD-TYPE 117   7  10  24
D66V10, multiclass
    clus
vv   17Q LOSS CNV 17Q LOSS WILD-TYPE
  R0            8                117
  R1            0                  7
  R2            2                 10
  RX            1                 24
D66V11, continuous

Clustering(67) Variable = 18p loss
D67V1, survival
                    sevent
clus2                  0   1
  18P LOSS CNV         7   4
  18P LOSS WILD-TYPE 117  15
      18P LOSS CNV 18P LOSS WILD-TYPE 
                11                132 
      18P LOSS CNV 18P LOSS WILD-TYPE 
                 4                 15 
$`18P LOSS CNV`
TCGA-BR-7723 TCGA-BR-8289 TCGA-BR-A4IY TCGA-CG-4440 TCGA-CG-4449 TCGA-CG-4469 
        4.54         0.26         0.39         4.01        19.07         7.07 
TCGA-CG-4477 TCGA-CG-5718 TCGA-D7-6519 TCGA-EQ-5647 TCGA-F1-6875 
        1.02         1.02        15.65         0.62        72.23 

$`18P LOSS WILD-TYPE`
TCGA-B7-5816 TCGA-B7-5818 TCGA-BR-6452 TCGA-BR-6455 TCGA-BR-6457 TCGA-BR-6458 
        5.62         0.10         0.95         1.41         1.35         1.35 
TCGA-BR-6563 TCGA-BR-6564 TCGA-BR-6565 TCGA-BR-6566 TCGA-BR-6705 TCGA-BR-6706 
        0.85         0.82         0.62         0.62         1.71         2.17 
TCGA-BR-6707 TCGA-BR-6709 TCGA-BR-6710 TCGA-BR-6801 TCGA-BR-6802 TCGA-BR-6803 
        0.99         1.22         0.66         1.12         0.76         0.66 
TCGA-BR-6852 TCGA-BR-7196 TCGA-BR-7197 TCGA-BR-7703 TCGA-BR-7704 TCGA-BR-7707 
        0.26         1.22         1.48         0.46         1.25         0.13 
TCGA-BR-7715 TCGA-BR-7716 TCGA-BR-7717 TCGA-BR-7722 TCGA-BR-7851 TCGA-BR-7901 
        1.05         0.82         0.69         0.16         0.99         0.95 
TCGA-BR-7957 TCGA-BR-7958 TCGA-BR-7959 TCGA-BR-8059 TCGA-BR-8060 TCGA-BR-8077 
        0.69         0.16         1.08         0.82         1.32         0.69 
TCGA-BR-8078 TCGA-BR-8080 TCGA-BR-8081 TCGA-BR-8284 TCGA-BR-8285 TCGA-BR-8286 
        0.95         0.49         0.46         0.72         0.26         0.43 
TCGA-BR-8291 TCGA-BR-8295 TCGA-BR-8296 TCGA-BR-8297 TCGA-BR-8592 TCGA-BR-A4IU 
        1.18         1.55         1.48         0.76         0.20         0.59 
TCGA-BR-A4IV TCGA-BR-A4IZ TCGA-BR-A4J1 TCGA-BR-A4J2 TCGA-BR-A4J4 TCGA-BR-A4J5 
        0.92         0.79         0.72         0.79         0.53         0.43 
TCGA-BR-A4J6 TCGA-BR-A4J8 TCGA-BR-A4J9 TCGA-BR-A4PF TCGA-BR-A4QI TCGA-BR-A4QL 
        0.13         0.23         0.10         0.72         0.49         2.24 
TCGA-CD-5798 TCGA-CD-5799 TCGA-CD-5800 TCGA-CD-5801 TCGA-CD-5802 TCGA-CD-5803 
        0.82         0.69         0.36         0.49         0.30         0.07 
TCGA-CG-4300 TCGA-CG-4301 TCGA-CG-4304 TCGA-CG-4305 TCGA-CG-4306 TCGA-CG-4436 
       20.02         3.02        27.02        15.95         1.02        52.96 
TCGA-CG-4437 TCGA-CG-4438 TCGA-CG-4441 TCGA-CG-4443 TCGA-CG-4444 TCGA-CG-4455 
        8.05        54.05        14.01        29.98        47.05        12.03 
TCGA-CG-4460 TCGA-CG-4462 TCGA-CG-4465 TCGA-CG-4466 TCGA-CG-4472 TCGA-CG-4474 
       21.99         1.02         8.98        18.94        12.00         1.02 
TCGA-CG-5716 TCGA-CG-5717 TCGA-CG-5719 TCGA-CG-5720 TCGA-CG-5721 TCGA-CG-5722 
        1.02         6.94         1.02         0.99         5.98         0.95 
TCGA-CG-5723 TCGA-CG-5724 TCGA-CG-5725 TCGA-CG-5726 TCGA-CG-5727 TCGA-CG-5728 
       70.06        12.03        15.02        28.96        31.04        65.10 
TCGA-CG-5730 TCGA-CG-5732 TCGA-CG-5733 TCGA-CG-5734 TCGA-D7-5577 TCGA-D7-5578 
        4.01        55.04        21.07         7.99         8.65         3.58 
TCGA-D7-5579 TCGA-D7-6518 TCGA-D7-6520 TCGA-D7-6521 TCGA-D7-6522 TCGA-D7-6524 
        4.54         9.80         9.63         8.19         6.90         0.69 
TCGA-D7-6525 TCGA-D7-6526 TCGA-D7-6527 TCGA-D7-6528 TCGA-D7-6815 TCGA-D7-6817 
        5.95         6.61         4.14         1.68         3.65         4.70 
TCGA-D7-6818 TCGA-D7-6820 TCGA-D7-6822 TCGA-EQ-8122 TCGA-F1-6177 TCGA-F1-6874 
        4.04         2.93         4.27         7.79         6.54         2.01 
TCGA-FP-7735 TCGA-FP-7829 TCGA-FP-7916 TCGA-FP-7998 TCGA-FP-8099 TCGA-FP-8209 
        0.39         0.20         3.02         3.58         1.02        59.05 
TCGA-FP-8210 TCGA-FP-8631 TCGA-HJ-7597 TCGA-IN-7806 TCGA-IN-7808 TCGA-IP-7968 
        5.03         0.56        26.43         6.87         3.55         2.53 

      18P LOSS CNV 18P LOSS WILD-TYPE 
              0.26               0.07 
      18P LOSS CNV 18P LOSS WILD-TYPE 
             72.23              70.06 
      18P LOSS CNV 18P LOSS WILD-TYPE 
             4.010              1.235 
[1] "0.3 - 72.2 (4.0)" "0.1 - 70.1 (1.2)"
        TCGA-B7-5816         TCGA-B7-5818         TCGA-BR-6452 
"18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" 
        TCGA-BR-6455         TCGA-BR-6457         TCGA-BR-6458 
"18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" 
        TCGA-BR-6563         TCGA-BR-6564         TCGA-BR-6565 
"18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" 
        TCGA-BR-6566         TCGA-BR-6705         TCGA-BR-6706 
"18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" 
        TCGA-BR-6707         TCGA-BR-6709         TCGA-BR-6710 
"18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" 
        TCGA-BR-6801         TCGA-BR-6802         TCGA-BR-6803 
"18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" 
        TCGA-BR-6852         TCGA-BR-7196         TCGA-BR-7197 
"18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" 
        TCGA-BR-7703         TCGA-BR-7704         TCGA-BR-7707 
"18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" 
        TCGA-BR-7715         TCGA-BR-7716         TCGA-BR-7717 
"18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" 
        TCGA-BR-7722         TCGA-BR-7723         TCGA-BR-7851 
"18P LOSS WILD-TYPE"       "18P LOSS CNV" "18P LOSS WILD-TYPE" 
        TCGA-BR-7901         TCGA-BR-7957         TCGA-BR-7958 
"18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" 
        TCGA-BR-7959         TCGA-BR-8059         TCGA-BR-8060 
"18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" 
        TCGA-BR-8077         TCGA-BR-8078         TCGA-BR-8080 
"18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" 
        TCGA-BR-8081         TCGA-BR-8284         TCGA-BR-8285 
"18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" 
        TCGA-BR-8286         TCGA-BR-8289         TCGA-BR-8291 
"18P LOSS WILD-TYPE"       "18P LOSS CNV" "18P LOSS WILD-TYPE" 
        TCGA-BR-8295         TCGA-BR-8296         TCGA-BR-8297 
"18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" 
        TCGA-BR-8592         TCGA-BR-A4IU         TCGA-BR-A4IV 
"18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" 
        TCGA-BR-A4IY         TCGA-BR-A4IZ         TCGA-BR-A4J1 
      "18P LOSS CNV" "18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" 
        TCGA-BR-A4J2         TCGA-BR-A4J4         TCGA-BR-A4J5 
"18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" 
        TCGA-BR-A4J6         TCGA-BR-A4J8         TCGA-BR-A4J9 
"18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" 
        TCGA-BR-A4PF         TCGA-BR-A4QI         TCGA-BR-A4QL 
"18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" 
        TCGA-CD-5798         TCGA-CD-5799         TCGA-CD-5800 
"18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" 
        TCGA-CD-5801         TCGA-CD-5802         TCGA-CD-5803 
"18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" 
        TCGA-CG-4300         TCGA-CG-4301         TCGA-CG-4304 
"18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" 
        TCGA-CG-4305         TCGA-CG-4306         TCGA-CG-4436 
"18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" 
        TCGA-CG-4437         TCGA-CG-4438         TCGA-CG-4440 
"18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE"       "18P LOSS CNV" 
        TCGA-CG-4441         TCGA-CG-4443         TCGA-CG-4444 
"18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" 
        TCGA-CG-4449         TCGA-CG-4455         TCGA-CG-4460 
      "18P LOSS CNV" "18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" 
        TCGA-CG-4462         TCGA-CG-4465         TCGA-CG-4466 
"18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" 
        TCGA-CG-4469         TCGA-CG-4472         TCGA-CG-4474 
      "18P LOSS CNV" "18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" 
        TCGA-CG-4477         TCGA-CG-5716         TCGA-CG-5717 
      "18P LOSS CNV" "18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" 
        TCGA-CG-5718         TCGA-CG-5719         TCGA-CG-5720 
      "18P LOSS CNV" "18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" 
        TCGA-CG-5721         TCGA-CG-5722         TCGA-CG-5723 
"18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" 
        TCGA-CG-5724         TCGA-CG-5725         TCGA-CG-5726 
"18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" 
        TCGA-CG-5727         TCGA-CG-5728         TCGA-CG-5730 
"18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" 
        TCGA-CG-5732         TCGA-CG-5733         TCGA-CG-5734 
"18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" 
        TCGA-D7-5577         TCGA-D7-5578         TCGA-D7-5579 
"18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" 
        TCGA-D7-6518         TCGA-D7-6519         TCGA-D7-6520 
"18P LOSS WILD-TYPE"       "18P LOSS CNV" "18P LOSS WILD-TYPE" 
        TCGA-D7-6521         TCGA-D7-6522         TCGA-D7-6524 
"18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" 
        TCGA-D7-6525         TCGA-D7-6526         TCGA-D7-6527 
"18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" 
        TCGA-D7-6528         TCGA-D7-6815         TCGA-D7-6817 
"18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" 
        TCGA-D7-6818         TCGA-D7-6820         TCGA-D7-6822 
"18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" 
        TCGA-EQ-5647         TCGA-EQ-8122         TCGA-F1-6177 
      "18P LOSS CNV" "18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" 
        TCGA-F1-6874         TCGA-F1-6875         TCGA-FP-7735 
"18P LOSS WILD-TYPE"       "18P LOSS CNV" "18P LOSS WILD-TYPE" 
        TCGA-FP-7829         TCGA-FP-7916         TCGA-FP-7998 
"18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" 
        TCGA-FP-8099         TCGA-FP-8209         TCGA-FP-8210 
"18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" 
        TCGA-FP-8631         TCGA-HJ-7597         TCGA-IN-7806 
"18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" 
        TCGA-IN-7808         TCGA-IP-7968 
"18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" 
        TCGA-B7-5816         TCGA-B7-5818         TCGA-BR-6452 
"18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" 
        TCGA-BR-6455         TCGA-BR-6457         TCGA-BR-6458 
"18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" 
        TCGA-BR-6563         TCGA-BR-6564         TCGA-BR-6565 
"18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" 
        TCGA-BR-6566         TCGA-BR-6705         TCGA-BR-6706 
"18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" 
        TCGA-BR-6707         TCGA-BR-6709         TCGA-BR-6710 
"18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" 
        TCGA-BR-6801         TCGA-BR-6802         TCGA-BR-6803 
"18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" 
        TCGA-BR-6852         TCGA-BR-7196         TCGA-BR-7197 
"18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" 
        TCGA-BR-7703         TCGA-BR-7704         TCGA-BR-7707 
"18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" 
        TCGA-BR-7715         TCGA-BR-7716         TCGA-BR-7717 
"18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" 
        TCGA-BR-7722         TCGA-BR-7723         TCGA-BR-7851 
"18P LOSS WILD-TYPE"       "18P LOSS CNV" "18P LOSS WILD-TYPE" 
        TCGA-BR-7901         TCGA-BR-7957         TCGA-BR-7958 
"18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" 
        TCGA-BR-7959         TCGA-BR-8059         TCGA-BR-8060 
"18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" 
        TCGA-BR-8077         TCGA-BR-8078         TCGA-BR-8080 
"18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" 
        TCGA-BR-8081         TCGA-BR-8284         TCGA-BR-8285 
"18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" 
        TCGA-BR-8286         TCGA-BR-8289         TCGA-BR-8291 
"18P LOSS WILD-TYPE"       "18P LOSS CNV" "18P LOSS WILD-TYPE" 
        TCGA-BR-8295         TCGA-BR-8296         TCGA-BR-8297 
"18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" 
        TCGA-BR-8592         TCGA-BR-A4IU         TCGA-BR-A4IV 
"18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" 
        TCGA-BR-A4IY         TCGA-BR-A4IZ         TCGA-BR-A4J1 
      "18P LOSS CNV" "18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" 
        TCGA-BR-A4J2         TCGA-BR-A4J4         TCGA-BR-A4J5 
"18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" 
        TCGA-BR-A4J6         TCGA-BR-A4J8         TCGA-BR-A4J9 
"18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" 
        TCGA-BR-A4PF         TCGA-BR-A4QI         TCGA-BR-A4QL 
"18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" 
        TCGA-CD-5798         TCGA-CD-5799         TCGA-CD-5800 
"18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" 
        TCGA-CD-5801         TCGA-CD-5802         TCGA-CD-5803 
"18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" 
        TCGA-CG-4300         TCGA-CG-4301         TCGA-CG-4304 
"18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" 
        TCGA-CG-4305         TCGA-CG-4306         TCGA-CG-4436 
"18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" 
        TCGA-CG-4437         TCGA-CG-4438         TCGA-CG-4440 
"18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE"       "18P LOSS CNV" 
        TCGA-CG-4441         TCGA-CG-4443         TCGA-CG-4444 
"18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" 
        TCGA-CG-4449         TCGA-CG-4455         TCGA-CG-4460 
      "18P LOSS CNV" "18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" 
        TCGA-CG-4462         TCGA-CG-4465         TCGA-CG-4466 
"18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" 
        TCGA-CG-4469         TCGA-CG-4472         TCGA-CG-4474 
      "18P LOSS CNV" "18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" 
        TCGA-CG-4477         TCGA-CG-5716         TCGA-CG-5717 
      "18P LOSS CNV" "18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" 
        TCGA-CG-5718         TCGA-CG-5719         TCGA-CG-5720 
      "18P LOSS CNV" "18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" 
        TCGA-CG-5721         TCGA-CG-5722         TCGA-CG-5723 
"18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" 
        TCGA-CG-5724         TCGA-CG-5725         TCGA-CG-5726 
"18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" 
        TCGA-CG-5727         TCGA-CG-5728         TCGA-CG-5730 
"18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" 
        TCGA-CG-5732         TCGA-CG-5733         TCGA-CG-5734 
"18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" 
        TCGA-D7-5577         TCGA-D7-5578         TCGA-D7-5579 
"18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" 
        TCGA-D7-6518         TCGA-D7-6519         TCGA-D7-6520 
"18P LOSS WILD-TYPE"       "18P LOSS CNV" "18P LOSS WILD-TYPE" 
        TCGA-D7-6521         TCGA-D7-6522         TCGA-D7-6524 
"18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" 
        TCGA-D7-6525         TCGA-D7-6526         TCGA-D7-6527 
"18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" 
        TCGA-D7-6528         TCGA-D7-6815         TCGA-D7-6817 
"18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" 
        TCGA-D7-6818         TCGA-D7-6820         TCGA-D7-6822 
"18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" 
        TCGA-EQ-5647         TCGA-EQ-8122         TCGA-F1-6177 
      "18P LOSS CNV" "18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" 
        TCGA-F1-6874         TCGA-F1-6875         TCGA-FP-7735 
"18P LOSS WILD-TYPE"       "18P LOSS CNV" "18P LOSS WILD-TYPE" 
        TCGA-FP-7829         TCGA-FP-7916         TCGA-FP-7998 
"18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" 
        TCGA-FP-8099         TCGA-FP-8209         TCGA-FP-8210 
"18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" 
        TCGA-FP-8631         TCGA-HJ-7597         TCGA-IN-7806 
"18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" 
        TCGA-IN-7808         TCGA-IP-7968 
"18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" 
        TCGA-B7-5816         TCGA-B7-5818         TCGA-BR-6452 
"18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" 
        TCGA-BR-6455         TCGA-BR-6457         TCGA-BR-6458 
"18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" 
        TCGA-BR-6563         TCGA-BR-6564         TCGA-BR-6565 
"18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" 
        TCGA-BR-6566         TCGA-BR-6705         TCGA-BR-6706 
"18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" 
        TCGA-BR-6707         TCGA-BR-6709         TCGA-BR-6710 
"18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" 
        TCGA-BR-6801         TCGA-BR-6802         TCGA-BR-6803 
"18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" 
        TCGA-BR-6852         TCGA-BR-7196         TCGA-BR-7197 
"18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" 
        TCGA-BR-7703         TCGA-BR-7704         TCGA-BR-7707 
"18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" 
        TCGA-BR-7715         TCGA-BR-7716         TCGA-BR-7717 
"18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" 
        TCGA-BR-7722         TCGA-BR-7723         TCGA-BR-7851 
"18P LOSS WILD-TYPE"       "18P LOSS CNV" "18P LOSS WILD-TYPE" 
        TCGA-BR-7901         TCGA-BR-7957         TCGA-BR-7958 
"18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" 
        TCGA-BR-7959         TCGA-BR-8059         TCGA-BR-8060 
"18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" 
        TCGA-BR-8077         TCGA-BR-8078         TCGA-BR-8080 
"18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" 
        TCGA-BR-8081         TCGA-BR-8284         TCGA-BR-8285 
"18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" 
        TCGA-BR-8286         TCGA-BR-8289         TCGA-BR-8291 
"18P LOSS WILD-TYPE"       "18P LOSS CNV" "18P LOSS WILD-TYPE" 
        TCGA-BR-8295         TCGA-BR-8296         TCGA-BR-8297 
"18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" 
        TCGA-BR-8592         TCGA-BR-A4IU         TCGA-BR-A4IV 
"18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" 
        TCGA-BR-A4IY         TCGA-BR-A4IZ         TCGA-BR-A4J1 
      "18P LOSS CNV" "18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" 
        TCGA-BR-A4J2         TCGA-BR-A4J4         TCGA-BR-A4J5 
"18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" 
        TCGA-BR-A4J6         TCGA-BR-A4J8         TCGA-BR-A4J9 
"18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" 
        TCGA-BR-A4PF         TCGA-BR-A4QI         TCGA-BR-A4QL 
"18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" 
        TCGA-CD-5798         TCGA-CD-5799         TCGA-CD-5800 
"18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" 
        TCGA-CD-5801         TCGA-CD-5802         TCGA-CD-5803 
"18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" 
        TCGA-CG-4300         TCGA-CG-4301         TCGA-CG-4304 
"18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" 
        TCGA-CG-4305         TCGA-CG-4306         TCGA-CG-4436 
"18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" 
        TCGA-CG-4437         TCGA-CG-4438         TCGA-CG-4440 
"18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE"       "18P LOSS CNV" 
        TCGA-CG-4441         TCGA-CG-4443         TCGA-CG-4444 
"18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" 
        TCGA-CG-4449         TCGA-CG-4455         TCGA-CG-4460 
      "18P LOSS CNV" "18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" 
        TCGA-CG-4462         TCGA-CG-4465         TCGA-CG-4466 
"18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" 
        TCGA-CG-4469         TCGA-CG-4472         TCGA-CG-4474 
      "18P LOSS CNV" "18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" 
        TCGA-CG-4477         TCGA-CG-5716         TCGA-CG-5717 
      "18P LOSS CNV" "18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" 
        TCGA-CG-5718         TCGA-CG-5719         TCGA-CG-5720 
      "18P LOSS CNV" "18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" 
        TCGA-CG-5721         TCGA-CG-5722         TCGA-CG-5723 
"18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" 
        TCGA-CG-5724         TCGA-CG-5725         TCGA-CG-5726 
"18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" 
        TCGA-CG-5727         TCGA-CG-5728         TCGA-CG-5730 
"18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" 
        TCGA-CG-5732         TCGA-CG-5733         TCGA-CG-5734 
"18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" 
        TCGA-D7-5577         TCGA-D7-5578         TCGA-D7-5579 
"18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" 
        TCGA-D7-6518         TCGA-D7-6519         TCGA-D7-6520 
"18P LOSS WILD-TYPE"       "18P LOSS CNV" "18P LOSS WILD-TYPE" 
        TCGA-D7-6521         TCGA-D7-6522         TCGA-D7-6524 
"18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" 
        TCGA-D7-6525         TCGA-D7-6526         TCGA-D7-6527 
"18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" 
        TCGA-D7-6528         TCGA-D7-6815         TCGA-D7-6817 
"18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" 
        TCGA-D7-6818         TCGA-D7-6820         TCGA-D7-6822 
"18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" 
        TCGA-EQ-5647         TCGA-EQ-8122         TCGA-F1-6177 
      "18P LOSS CNV" "18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" 
        TCGA-F1-6874         TCGA-F1-6875         TCGA-FP-7735 
"18P LOSS WILD-TYPE"       "18P LOSS CNV" "18P LOSS WILD-TYPE" 
        TCGA-FP-7829         TCGA-FP-7916         TCGA-FP-7998 
"18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" 
        TCGA-FP-8099         TCGA-FP-8209         TCGA-FP-8210 
"18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" 
        TCGA-FP-8631         TCGA-HJ-7597         TCGA-IN-7806 
"18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" 
        TCGA-IN-7808         TCGA-IP-7968 
"18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" 
[1] "hr=" "1.7"
D67V2, continuous
D67V3, binary
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  18P LOSS CNV          5    9
  18P LOSS WILD-TYPE   67   99
        clus
vv       18P LOSS CNV 18P LOSS WILD-TYPE
  FEMALE            5                 67
  MALE              9                 99
                    vv
clus                 STOMACH  ADENOCARCINOMA  DIFFUSE TYPE
  18P LOSS CNV                                           0
  18P LOSS WILD-TYPE                                    10
                    vv
clus                 STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  18P LOSS CNV                                                            1
  18P LOSS WILD-TYPE                                                     15
                    vv
clus                 STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  18P LOSS CNV                                                                       1
  18P LOSS WILD-TYPE                                                                 7
                    vv
clus                 STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE
  18P LOSS CNV                                                              0
  18P LOSS WILD-TYPE                                                        3
                    vv
clus                 STOMACH ADENOCARCINOMA  SIGNET RING TYPE
  18P LOSS CNV                                              0
  18P LOSS WILD-TYPE                                        1
                    vv
clus                 STOMACH ADENOCARCINOMA - DIFFUSE TYPE
  18P LOSS CNV                                           1
  18P LOSS WILD-TYPE                                    15
                    vv
clus                 STOMACH ADENOCARCINOMA - NOT OTHERWISE SPECIFIED (NOS)
  18P LOSS CNV                                                            5
  18P LOSS WILD-TYPE                                                     68
                    vv
clus                 STOMACH INTESTINAL ADENOCARCINOMA - MUCINOUS TYPE
  18P LOSS CNV                                                       1
  18P LOSS WILD-TYPE                                                 6
                    vv
clus                 STOMACH INTESTINAL ADENOCARCINOMA - PAPILLARY TYPE
  18P LOSS CNV                                                        0
  18P LOSS WILD-TYPE                                                  3
                    vv
clus                 STOMACH INTESTINAL ADENOCARCINOMA - TUBULAR TYPE
  18P LOSS CNV                                                      1
  18P LOSS WILD-TYPE                                                9
                    vv
clus                 STOMACH INTESTINAL ADENOCARCINOMA - TYPE NOT OTHERWISE SPECIFIED (NOS)
  18P LOSS CNV                                                                            4
  18P LOSS WILD-TYPE                                                                     24
D67V4, multiclass
                    vv
clus                 T1 T2 T3 T4
  18P LOSS CNV        0  7  3  1
  18P LOSS WILD-TYPE  6 45 53 17
D67V5, multiclass
    clus
vv   18P LOSS CNV 18P LOSS WILD-TYPE
  T1            0                  6
  T2            7                 45
  T3            3                 53
  T4            1                 17
                    vv
clus                 N0 N1 N2 N3
  18P LOSS CNV        2  4  1  3
  18P LOSS WILD-TYPE 42 45 22 12
D67V6, multiclass
    clus
vv   18P LOSS CNV 18P LOSS WILD-TYPE
  N0            2                 42
  N1            4                 45
  N2            1                 22
  N3            3                 12
                    vv
clus                  M0  M1  MX
  18P LOSS CNV        10   2   0
  18P LOSS WILD-TYPE 108  14   8
D67V7, multiclass
    clus
vv   18P LOSS CNV 18P LOSS WILD-TYPE
  M0           10                108
  M1            2                 14
  MX            0                  8
                    vv
clus                  I II III IV
  18P LOSS CNV        2  4   1  3
  18P LOSS WILD-TYPE 22 33  38 23
D67V8, multiclass
     clus
vv    18P LOSS CNV 18P LOSS WILD-TYPE
  I              2                 22
  II             4                 33
  III            1                 38
  IV             3                 23
D67V9, binary
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  18P LOSS CNV          0   14
  18P LOSS WILD-TYPE    5  161
     clus
vv    18P LOSS CNV 18P LOSS WILD-TYPE
  NO             0                  5
  YES           14                161
                    vv
clus                  R0  R1  R2  RX
  18P LOSS CNV         8   1   2   3
  18P LOSS WILD-TYPE 117   6  10  22
D67V10, multiclass
    clus
vv   18P LOSS CNV 18P LOSS WILD-TYPE
  R0            8                117
  R1            1                  6
  R2            2                 10
  RX            3                 22
D67V11, continuous

Clustering(68) Variable = 18q loss
D68V1, survival
                    sevent
clus2                  0   1
  18Q LOSS CNV        17   4
  18Q LOSS WILD-TYPE 107  15
      18Q LOSS CNV 18Q LOSS WILD-TYPE 
                21                122 
      18Q LOSS CNV 18Q LOSS WILD-TYPE 
                 4                 15 
$`18Q LOSS CNV`
TCGA-B7-5818 TCGA-BR-7723 TCGA-BR-8060 TCGA-BR-A4IY TCGA-BR-A4J6 TCGA-CD-5802 
        0.10         4.54         1.32         0.39         0.13         0.30 
TCGA-CG-4301 TCGA-CG-4438 TCGA-CG-4440 TCGA-CG-4449 TCGA-CG-4469 TCGA-CG-4477 
        3.02        54.05         4.01        19.07         7.07         1.02 
TCGA-CG-5718 TCGA-CG-5724 TCGA-CG-5730 TCGA-D7-5577 TCGA-D7-6519 TCGA-D7-6521 
        1.02        12.03         4.01         8.65        15.65         8.19 
TCGA-EQ-5647 TCGA-EQ-8122 TCGA-FP-7829 
        0.62         7.79         0.20 

$`18Q LOSS WILD-TYPE`
TCGA-B7-5816 TCGA-BR-6452 TCGA-BR-6455 TCGA-BR-6457 TCGA-BR-6458 TCGA-BR-6563 
        5.62         0.95         1.41         1.35         1.35         0.85 
TCGA-BR-6564 TCGA-BR-6565 TCGA-BR-6566 TCGA-BR-6705 TCGA-BR-6706 TCGA-BR-6707 
        0.82         0.62         0.62         1.71         2.17         0.99 
TCGA-BR-6709 TCGA-BR-6710 TCGA-BR-6801 TCGA-BR-6802 TCGA-BR-6803 TCGA-BR-6852 
        1.22         0.66         1.12         0.76         0.66         0.26 
TCGA-BR-7196 TCGA-BR-7197 TCGA-BR-7703 TCGA-BR-7704 TCGA-BR-7707 TCGA-BR-7715 
        1.22         1.48         0.46         1.25         0.13         1.05 
TCGA-BR-7716 TCGA-BR-7717 TCGA-BR-7722 TCGA-BR-7851 TCGA-BR-7901 TCGA-BR-7957 
        0.82         0.69         0.16         0.99         0.95         0.69 
TCGA-BR-7958 TCGA-BR-7959 TCGA-BR-8059 TCGA-BR-8077 TCGA-BR-8078 TCGA-BR-8080 
        0.16         1.08         0.82         0.69         0.95         0.49 
TCGA-BR-8081 TCGA-BR-8284 TCGA-BR-8285 TCGA-BR-8286 TCGA-BR-8289 TCGA-BR-8291 
        0.46         0.72         0.26         0.43         0.26         1.18 
TCGA-BR-8295 TCGA-BR-8296 TCGA-BR-8297 TCGA-BR-8592 TCGA-BR-A4IU TCGA-BR-A4IV 
        1.55         1.48         0.76         0.20         0.59         0.92 
TCGA-BR-A4IZ TCGA-BR-A4J1 TCGA-BR-A4J2 TCGA-BR-A4J4 TCGA-BR-A4J5 TCGA-BR-A4J8 
        0.79         0.72         0.79         0.53         0.43         0.23 
TCGA-BR-A4J9 TCGA-BR-A4PF TCGA-BR-A4QI TCGA-BR-A4QL TCGA-CD-5798 TCGA-CD-5799 
        0.10         0.72         0.49         2.24         0.82         0.69 
TCGA-CD-5800 TCGA-CD-5801 TCGA-CD-5803 TCGA-CG-4300 TCGA-CG-4304 TCGA-CG-4305 
        0.36         0.49         0.07        20.02        27.02        15.95 
TCGA-CG-4306 TCGA-CG-4436 TCGA-CG-4437 TCGA-CG-4441 TCGA-CG-4443 TCGA-CG-4444 
        1.02        52.96         8.05        14.01        29.98        47.05 
TCGA-CG-4455 TCGA-CG-4460 TCGA-CG-4462 TCGA-CG-4465 TCGA-CG-4466 TCGA-CG-4472 
       12.03        21.99         1.02         8.98        18.94        12.00 
TCGA-CG-4474 TCGA-CG-5716 TCGA-CG-5717 TCGA-CG-5719 TCGA-CG-5720 TCGA-CG-5721 
        1.02         1.02         6.94         1.02         0.99         5.98 
TCGA-CG-5722 TCGA-CG-5723 TCGA-CG-5725 TCGA-CG-5726 TCGA-CG-5727 TCGA-CG-5728 
        0.95        70.06        15.02        28.96        31.04        65.10 
TCGA-CG-5732 TCGA-CG-5733 TCGA-CG-5734 TCGA-D7-5578 TCGA-D7-5579 TCGA-D7-6518 
       55.04        21.07         7.99         3.58         4.54         9.80 
TCGA-D7-6520 TCGA-D7-6522 TCGA-D7-6524 TCGA-D7-6525 TCGA-D7-6526 TCGA-D7-6527 
        9.63         6.90         0.69         5.95         6.61         4.14 
TCGA-D7-6528 TCGA-D7-6815 TCGA-D7-6817 TCGA-D7-6818 TCGA-D7-6820 TCGA-D7-6822 
        1.68         3.65         4.70         4.04         2.93         4.27 
TCGA-F1-6177 TCGA-F1-6874 TCGA-F1-6875 TCGA-FP-7735 TCGA-FP-7916 TCGA-FP-7998 
        6.54         2.01        72.23         0.39         3.02         3.58 
TCGA-FP-8099 TCGA-FP-8209 TCGA-FP-8210 TCGA-FP-8631 TCGA-HJ-7597 TCGA-IN-7806 
        1.02        59.05         5.03         0.56        26.43         6.87 
TCGA-IN-7808 TCGA-IP-7968 
        3.55         2.53 

      18Q LOSS CNV 18Q LOSS WILD-TYPE 
              0.10               0.07 
      18Q LOSS CNV 18Q LOSS WILD-TYPE 
             54.05              72.23 
      18Q LOSS CNV 18Q LOSS WILD-TYPE 
              4.01               1.20 
[1] "0.1 - 54.0 (4.0)" "0.1 - 72.2 (1.2)"
        TCGA-B7-5816         TCGA-B7-5818         TCGA-BR-6452 
"18Q LOSS WILD-TYPE"       "18Q LOSS CNV" "18Q LOSS WILD-TYPE" 
        TCGA-BR-6455         TCGA-BR-6457         TCGA-BR-6458 
"18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" 
        TCGA-BR-6563         TCGA-BR-6564         TCGA-BR-6565 
"18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" 
        TCGA-BR-6566         TCGA-BR-6705         TCGA-BR-6706 
"18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" 
        TCGA-BR-6707         TCGA-BR-6709         TCGA-BR-6710 
"18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" 
        TCGA-BR-6801         TCGA-BR-6802         TCGA-BR-6803 
"18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" 
        TCGA-BR-6852         TCGA-BR-7196         TCGA-BR-7197 
"18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" 
        TCGA-BR-7703         TCGA-BR-7704         TCGA-BR-7707 
"18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" 
        TCGA-BR-7715         TCGA-BR-7716         TCGA-BR-7717 
"18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" 
        TCGA-BR-7722         TCGA-BR-7723         TCGA-BR-7851 
"18Q LOSS WILD-TYPE"       "18Q LOSS CNV" "18Q LOSS WILD-TYPE" 
        TCGA-BR-7901         TCGA-BR-7957         TCGA-BR-7958 
"18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" 
        TCGA-BR-7959         TCGA-BR-8059         TCGA-BR-8060 
"18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE"       "18Q LOSS CNV" 
        TCGA-BR-8077         TCGA-BR-8078         TCGA-BR-8080 
"18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" 
        TCGA-BR-8081         TCGA-BR-8284         TCGA-BR-8285 
"18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" 
        TCGA-BR-8286         TCGA-BR-8289         TCGA-BR-8291 
"18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" 
        TCGA-BR-8295         TCGA-BR-8296         TCGA-BR-8297 
"18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" 
        TCGA-BR-8592         TCGA-BR-A4IU         TCGA-BR-A4IV 
"18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" 
        TCGA-BR-A4IY         TCGA-BR-A4IZ         TCGA-BR-A4J1 
      "18Q LOSS CNV" "18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" 
        TCGA-BR-A4J2         TCGA-BR-A4J4         TCGA-BR-A4J5 
"18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" 
        TCGA-BR-A4J6         TCGA-BR-A4J8         TCGA-BR-A4J9 
      "18Q LOSS CNV" "18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" 
        TCGA-BR-A4PF         TCGA-BR-A4QI         TCGA-BR-A4QL 
"18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" 
        TCGA-CD-5798         TCGA-CD-5799         TCGA-CD-5800 
"18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" 
        TCGA-CD-5801         TCGA-CD-5802         TCGA-CD-5803 
"18Q LOSS WILD-TYPE"       "18Q LOSS CNV" "18Q LOSS WILD-TYPE" 
        TCGA-CG-4300         TCGA-CG-4301         TCGA-CG-4304 
"18Q LOSS WILD-TYPE"       "18Q LOSS CNV" "18Q LOSS WILD-TYPE" 
        TCGA-CG-4305         TCGA-CG-4306         TCGA-CG-4436 
"18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" 
        TCGA-CG-4437         TCGA-CG-4438         TCGA-CG-4440 
"18Q LOSS WILD-TYPE"       "18Q LOSS CNV"       "18Q LOSS CNV" 
        TCGA-CG-4441         TCGA-CG-4443         TCGA-CG-4444 
"18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" 
        TCGA-CG-4449         TCGA-CG-4455         TCGA-CG-4460 
      "18Q LOSS CNV" "18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" 
        TCGA-CG-4462         TCGA-CG-4465         TCGA-CG-4466 
"18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" 
        TCGA-CG-4469         TCGA-CG-4472         TCGA-CG-4474 
      "18Q LOSS CNV" "18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" 
        TCGA-CG-4477         TCGA-CG-5716         TCGA-CG-5717 
      "18Q LOSS CNV" "18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" 
        TCGA-CG-5718         TCGA-CG-5719         TCGA-CG-5720 
      "18Q LOSS CNV" "18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" 
        TCGA-CG-5721         TCGA-CG-5722         TCGA-CG-5723 
"18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" 
        TCGA-CG-5724         TCGA-CG-5725         TCGA-CG-5726 
      "18Q LOSS CNV" "18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" 
        TCGA-CG-5727         TCGA-CG-5728         TCGA-CG-5730 
"18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE"       "18Q LOSS CNV" 
        TCGA-CG-5732         TCGA-CG-5733         TCGA-CG-5734 
"18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" 
        TCGA-D7-5577         TCGA-D7-5578         TCGA-D7-5579 
      "18Q LOSS CNV" "18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" 
        TCGA-D7-6518         TCGA-D7-6519         TCGA-D7-6520 
"18Q LOSS WILD-TYPE"       "18Q LOSS CNV" "18Q LOSS WILD-TYPE" 
        TCGA-D7-6521         TCGA-D7-6522         TCGA-D7-6524 
      "18Q LOSS CNV" "18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" 
        TCGA-D7-6525         TCGA-D7-6526         TCGA-D7-6527 
"18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" 
        TCGA-D7-6528         TCGA-D7-6815         TCGA-D7-6817 
"18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" 
        TCGA-D7-6818         TCGA-D7-6820         TCGA-D7-6822 
"18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" 
        TCGA-EQ-5647         TCGA-EQ-8122         TCGA-F1-6177 
      "18Q LOSS CNV"       "18Q LOSS CNV" "18Q LOSS WILD-TYPE" 
        TCGA-F1-6874         TCGA-F1-6875         TCGA-FP-7735 
"18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" 
        TCGA-FP-7829         TCGA-FP-7916         TCGA-FP-7998 
      "18Q LOSS CNV" "18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" 
        TCGA-FP-8099         TCGA-FP-8209         TCGA-FP-8210 
"18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" 
        TCGA-FP-8631         TCGA-HJ-7597         TCGA-IN-7806 
"18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" 
        TCGA-IN-7808         TCGA-IP-7968 
"18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" 
        TCGA-B7-5816         TCGA-B7-5818         TCGA-BR-6452 
"18Q LOSS WILD-TYPE"       "18Q LOSS CNV" "18Q LOSS WILD-TYPE" 
        TCGA-BR-6455         TCGA-BR-6457         TCGA-BR-6458 
"18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" 
        TCGA-BR-6563         TCGA-BR-6564         TCGA-BR-6565 
"18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" 
        TCGA-BR-6566         TCGA-BR-6705         TCGA-BR-6706 
"18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" 
        TCGA-BR-6707         TCGA-BR-6709         TCGA-BR-6710 
"18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" 
        TCGA-BR-6801         TCGA-BR-6802         TCGA-BR-6803 
"18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" 
        TCGA-BR-6852         TCGA-BR-7196         TCGA-BR-7197 
"18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" 
        TCGA-BR-7703         TCGA-BR-7704         TCGA-BR-7707 
"18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" 
        TCGA-BR-7715         TCGA-BR-7716         TCGA-BR-7717 
"18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" 
        TCGA-BR-7722         TCGA-BR-7723         TCGA-BR-7851 
"18Q LOSS WILD-TYPE"       "18Q LOSS CNV" "18Q LOSS WILD-TYPE" 
        TCGA-BR-7901         TCGA-BR-7957         TCGA-BR-7958 
"18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" 
        TCGA-BR-7959         TCGA-BR-8059         TCGA-BR-8060 
"18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE"       "18Q LOSS CNV" 
        TCGA-BR-8077         TCGA-BR-8078         TCGA-BR-8080 
"18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" 
        TCGA-BR-8081         TCGA-BR-8284         TCGA-BR-8285 
"18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" 
        TCGA-BR-8286         TCGA-BR-8289         TCGA-BR-8291 
"18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" 
        TCGA-BR-8295         TCGA-BR-8296         TCGA-BR-8297 
"18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" 
        TCGA-BR-8592         TCGA-BR-A4IU         TCGA-BR-A4IV 
"18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" 
        TCGA-BR-A4IY         TCGA-BR-A4IZ         TCGA-BR-A4J1 
      "18Q LOSS CNV" "18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" 
        TCGA-BR-A4J2         TCGA-BR-A4J4         TCGA-BR-A4J5 
"18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" 
        TCGA-BR-A4J6         TCGA-BR-A4J8         TCGA-BR-A4J9 
      "18Q LOSS CNV" "18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" 
        TCGA-BR-A4PF         TCGA-BR-A4QI         TCGA-BR-A4QL 
"18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" 
        TCGA-CD-5798         TCGA-CD-5799         TCGA-CD-5800 
"18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" 
        TCGA-CD-5801         TCGA-CD-5802         TCGA-CD-5803 
"18Q LOSS WILD-TYPE"       "18Q LOSS CNV" "18Q LOSS WILD-TYPE" 
        TCGA-CG-4300         TCGA-CG-4301         TCGA-CG-4304 
"18Q LOSS WILD-TYPE"       "18Q LOSS CNV" "18Q LOSS WILD-TYPE" 
        TCGA-CG-4305         TCGA-CG-4306         TCGA-CG-4436 
"18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" 
        TCGA-CG-4437         TCGA-CG-4438         TCGA-CG-4440 
"18Q LOSS WILD-TYPE"       "18Q LOSS CNV"       "18Q LOSS CNV" 
        TCGA-CG-4441         TCGA-CG-4443         TCGA-CG-4444 
"18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" 
        TCGA-CG-4449         TCGA-CG-4455         TCGA-CG-4460 
      "18Q LOSS CNV" "18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" 
        TCGA-CG-4462         TCGA-CG-4465         TCGA-CG-4466 
"18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" 
        TCGA-CG-4469         TCGA-CG-4472         TCGA-CG-4474 
      "18Q LOSS CNV" "18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" 
        TCGA-CG-4477         TCGA-CG-5716         TCGA-CG-5717 
      "18Q LOSS CNV" "18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" 
        TCGA-CG-5718         TCGA-CG-5719         TCGA-CG-5720 
      "18Q LOSS CNV" "18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" 
        TCGA-CG-5721         TCGA-CG-5722         TCGA-CG-5723 
"18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" 
        TCGA-CG-5724         TCGA-CG-5725         TCGA-CG-5726 
      "18Q LOSS CNV" "18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" 
        TCGA-CG-5727         TCGA-CG-5728         TCGA-CG-5730 
"18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE"       "18Q LOSS CNV" 
        TCGA-CG-5732         TCGA-CG-5733         TCGA-CG-5734 
"18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" 
        TCGA-D7-5577         TCGA-D7-5578         TCGA-D7-5579 
      "18Q LOSS CNV" "18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" 
        TCGA-D7-6518         TCGA-D7-6519         TCGA-D7-6520 
"18Q LOSS WILD-TYPE"       "18Q LOSS CNV" "18Q LOSS WILD-TYPE" 
        TCGA-D7-6521         TCGA-D7-6522         TCGA-D7-6524 
      "18Q LOSS CNV" "18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" 
        TCGA-D7-6525         TCGA-D7-6526         TCGA-D7-6527 
"18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" 
        TCGA-D7-6528         TCGA-D7-6815         TCGA-D7-6817 
"18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" 
        TCGA-D7-6818         TCGA-D7-6820         TCGA-D7-6822 
"18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" 
        TCGA-EQ-5647         TCGA-EQ-8122         TCGA-F1-6177 
      "18Q LOSS CNV"       "18Q LOSS CNV" "18Q LOSS WILD-TYPE" 
        TCGA-F1-6874         TCGA-F1-6875         TCGA-FP-7735 
"18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" 
        TCGA-FP-7829         TCGA-FP-7916         TCGA-FP-7998 
      "18Q LOSS CNV" "18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" 
        TCGA-FP-8099         TCGA-FP-8209         TCGA-FP-8210 
"18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" 
        TCGA-FP-8631         TCGA-HJ-7597         TCGA-IN-7806 
"18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" 
        TCGA-IN-7808         TCGA-IP-7968 
"18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" 
        TCGA-B7-5816         TCGA-B7-5818         TCGA-BR-6452 
"18Q LOSS WILD-TYPE"       "18Q LOSS CNV" "18Q LOSS WILD-TYPE" 
        TCGA-BR-6455         TCGA-BR-6457         TCGA-BR-6458 
"18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" 
        TCGA-BR-6563         TCGA-BR-6564         TCGA-BR-6565 
"18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" 
        TCGA-BR-6566         TCGA-BR-6705         TCGA-BR-6706 
"18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" 
        TCGA-BR-6707         TCGA-BR-6709         TCGA-BR-6710 
"18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" 
        TCGA-BR-6801         TCGA-BR-6802         TCGA-BR-6803 
"18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" 
        TCGA-BR-6852         TCGA-BR-7196         TCGA-BR-7197 
"18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" 
        TCGA-BR-7703         TCGA-BR-7704         TCGA-BR-7707 
"18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" 
        TCGA-BR-7715         TCGA-BR-7716         TCGA-BR-7717 
"18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" 
        TCGA-BR-7722         TCGA-BR-7723         TCGA-BR-7851 
"18Q LOSS WILD-TYPE"       "18Q LOSS CNV" "18Q LOSS WILD-TYPE" 
        TCGA-BR-7901         TCGA-BR-7957         TCGA-BR-7958 
"18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" 
        TCGA-BR-7959         TCGA-BR-8059         TCGA-BR-8060 
"18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE"       "18Q LOSS CNV" 
        TCGA-BR-8077         TCGA-BR-8078         TCGA-BR-8080 
"18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" 
        TCGA-BR-8081         TCGA-BR-8284         TCGA-BR-8285 
"18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" 
        TCGA-BR-8286         TCGA-BR-8289         TCGA-BR-8291 
"18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" 
        TCGA-BR-8295         TCGA-BR-8296         TCGA-BR-8297 
"18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" 
        TCGA-BR-8592         TCGA-BR-A4IU         TCGA-BR-A4IV 
"18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" 
        TCGA-BR-A4IY         TCGA-BR-A4IZ         TCGA-BR-A4J1 
      "18Q LOSS CNV" "18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" 
        TCGA-BR-A4J2         TCGA-BR-A4J4         TCGA-BR-A4J5 
"18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" 
        TCGA-BR-A4J6         TCGA-BR-A4J8         TCGA-BR-A4J9 
      "18Q LOSS CNV" "18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" 
        TCGA-BR-A4PF         TCGA-BR-A4QI         TCGA-BR-A4QL 
"18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" 
        TCGA-CD-5798         TCGA-CD-5799         TCGA-CD-5800 
"18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" 
        TCGA-CD-5801         TCGA-CD-5802         TCGA-CD-5803 
"18Q LOSS WILD-TYPE"       "18Q LOSS CNV" "18Q LOSS WILD-TYPE" 
        TCGA-CG-4300         TCGA-CG-4301         TCGA-CG-4304 
"18Q LOSS WILD-TYPE"       "18Q LOSS CNV" "18Q LOSS WILD-TYPE" 
        TCGA-CG-4305         TCGA-CG-4306         TCGA-CG-4436 
"18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" 
        TCGA-CG-4437         TCGA-CG-4438         TCGA-CG-4440 
"18Q LOSS WILD-TYPE"       "18Q LOSS CNV"       "18Q LOSS CNV" 
        TCGA-CG-4441         TCGA-CG-4443         TCGA-CG-4444 
"18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" 
        TCGA-CG-4449         TCGA-CG-4455         TCGA-CG-4460 
      "18Q LOSS CNV" "18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" 
        TCGA-CG-4462         TCGA-CG-4465         TCGA-CG-4466 
"18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" 
        TCGA-CG-4469         TCGA-CG-4472         TCGA-CG-4474 
      "18Q LOSS CNV" "18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" 
        TCGA-CG-4477         TCGA-CG-5716         TCGA-CG-5717 
      "18Q LOSS CNV" "18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" 
        TCGA-CG-5718         TCGA-CG-5719         TCGA-CG-5720 
      "18Q LOSS CNV" "18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" 
        TCGA-CG-5721         TCGA-CG-5722         TCGA-CG-5723 
"18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" 
        TCGA-CG-5724         TCGA-CG-5725         TCGA-CG-5726 
      "18Q LOSS CNV" "18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" 
        TCGA-CG-5727         TCGA-CG-5728         TCGA-CG-5730 
"18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE"       "18Q LOSS CNV" 
        TCGA-CG-5732         TCGA-CG-5733         TCGA-CG-5734 
"18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" 
        TCGA-D7-5577         TCGA-D7-5578         TCGA-D7-5579 
      "18Q LOSS CNV" "18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" 
        TCGA-D7-6518         TCGA-D7-6519         TCGA-D7-6520 
"18Q LOSS WILD-TYPE"       "18Q LOSS CNV" "18Q LOSS WILD-TYPE" 
        TCGA-D7-6521         TCGA-D7-6522         TCGA-D7-6524 
      "18Q LOSS CNV" "18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" 
        TCGA-D7-6525         TCGA-D7-6526         TCGA-D7-6527 
"18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" 
        TCGA-D7-6528         TCGA-D7-6815         TCGA-D7-6817 
"18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" 
        TCGA-D7-6818         TCGA-D7-6820         TCGA-D7-6822 
"18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" 
        TCGA-EQ-5647         TCGA-EQ-8122         TCGA-F1-6177 
      "18Q LOSS CNV"       "18Q LOSS CNV" "18Q LOSS WILD-TYPE" 
        TCGA-F1-6874         TCGA-F1-6875         TCGA-FP-7735 
"18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" 
        TCGA-FP-7829         TCGA-FP-7916         TCGA-FP-7998 
      "18Q LOSS CNV" "18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" 
        TCGA-FP-8099         TCGA-FP-8209         TCGA-FP-8210 
"18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" 
        TCGA-FP-8631         TCGA-HJ-7597         TCGA-IN-7806 
"18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" 
        TCGA-IN-7808         TCGA-IP-7968 
"18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" 
[1] "hr=" "1.8"
D68V2, continuous
D68V3, binary
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  18Q LOSS CNV         11   17
  18Q LOSS WILD-TYPE   61   91
        clus
vv       18Q LOSS CNV 18Q LOSS WILD-TYPE
  FEMALE           11                 61
  MALE             17                 91
                    vv
clus                 STOMACH  ADENOCARCINOMA  DIFFUSE TYPE
  18Q LOSS CNV                                           0
  18Q LOSS WILD-TYPE                                    10
                    vv
clus                 STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  18Q LOSS CNV                                                            3
  18Q LOSS WILD-TYPE                                                     13
                    vv
clus                 STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  18Q LOSS CNV                                                                       1
  18Q LOSS WILD-TYPE                                                                 7
                    vv
clus                 STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE
  18Q LOSS CNV                                                              0
  18Q LOSS WILD-TYPE                                                        3
                    vv
clus                 STOMACH ADENOCARCINOMA  SIGNET RING TYPE
  18Q LOSS CNV                                              0
  18Q LOSS WILD-TYPE                                        1
                    vv
clus                 STOMACH ADENOCARCINOMA - DIFFUSE TYPE
  18Q LOSS CNV                                           4
  18Q LOSS WILD-TYPE                                    12
                    vv
clus                 STOMACH ADENOCARCINOMA - NOT OTHERWISE SPECIFIED (NOS)
  18Q LOSS CNV                                                            9
  18Q LOSS WILD-TYPE                                                     64
                    vv
clus                 STOMACH INTESTINAL ADENOCARCINOMA - MUCINOUS TYPE
  18Q LOSS CNV                                                       2
  18Q LOSS WILD-TYPE                                                 5
                    vv
clus                 STOMACH INTESTINAL ADENOCARCINOMA - PAPILLARY TYPE
  18Q LOSS CNV                                                        0
  18Q LOSS WILD-TYPE                                                  3
                    vv
clus                 STOMACH INTESTINAL ADENOCARCINOMA - TUBULAR TYPE
  18Q LOSS CNV                                                      2
  18Q LOSS WILD-TYPE                                                8
                    vv
clus                 STOMACH INTESTINAL ADENOCARCINOMA - TYPE NOT OTHERWISE SPECIFIED (NOS)
  18Q LOSS CNV                                                                            6
  18Q LOSS WILD-TYPE                                                                     22
D68V4, multiclass
                    vv
clus                 T1 T2 T3 T4
  18Q LOSS CNV        0 11  8  3
  18Q LOSS WILD-TYPE  6 41 48 15
D68V5, multiclass
    clus
vv   18Q LOSS CNV 18Q LOSS WILD-TYPE
  T1            0                  6
  T2           11                 41
  T3            8                 48
  T4            3                 15
                    vv
clus                 N0 N1 N2 N3
  18Q LOSS CNV        4 10  3  5
  18Q LOSS WILD-TYPE 40 39 20 10
D68V6, multiclass
    clus
vv   18Q LOSS CNV 18Q LOSS WILD-TYPE
  N0            4                 40
  N1           10                 39
  N2            3                 20
  N3            5                 10
                    vv
clus                 M0 M1 MX
  18Q LOSS CNV       19  5  0
  18Q LOSS WILD-TYPE 99 11  8
D68V7, multiclass
    clus
vv   18Q LOSS CNV 18Q LOSS WILD-TYPE
  M0           19                 99
  M1            5                 11
  MX            0                  8
                    vv
clus                  I II III IV
  18Q LOSS CNV        3  6   5  7
  18Q LOSS WILD-TYPE 21 31  34 19
D68V8, multiclass
     clus
vv    18Q LOSS CNV 18Q LOSS WILD-TYPE
  I              3                 21
  II             6                 31
  III            5                 34
  IV             7                 19
D68V9, binary
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  18Q LOSS CNV          0   28
  18Q LOSS WILD-TYPE    5  147
     clus
vv    18Q LOSS CNV 18Q LOSS WILD-TYPE
  NO             0                  5
  YES           28                147
                    vv
clus                  R0  R1  R2  RX
  18Q LOSS CNV        14   2   5   5
  18Q LOSS WILD-TYPE 111   5   7  20
D68V10, multiclass
    clus
vv   18Q LOSS CNV 18Q LOSS WILD-TYPE
  R0           14                111
  R1            2                  5
  R2            5                  7
  RX            5                 20
D68V11, continuous

Clustering(69) Variable = 19p loss
D69V1, survival
                    sevent
clus2                  0   1
  19P LOSS CNV        14   4
  19P LOSS WILD-TYPE 110  15
      19P LOSS CNV 19P LOSS WILD-TYPE 
                18                125 
      19P LOSS CNV 19P LOSS WILD-TYPE 
                 4                 15 
$`19P LOSS CNV`
TCGA-BR-6458 TCGA-BR-6565 TCGA-BR-7723 TCGA-BR-8060 TCGA-BR-8295 TCGA-BR-A4J1 
        1.35         0.62         4.54         1.32         1.55         0.72 
TCGA-CG-4436 TCGA-CG-4438 TCGA-CG-4440 TCGA-CG-4443 TCGA-CG-4466 TCGA-CG-5725 
       52.96        54.05         4.01        29.98        18.94        15.02 
TCGA-CG-5732 TCGA-D7-6520 TCGA-D7-6525 TCGA-D7-6820 TCGA-EQ-5647 TCGA-FP-8631 
       55.04         9.63         5.95         2.93         0.62         0.56 

$`19P LOSS WILD-TYPE`
TCGA-B7-5816 TCGA-B7-5818 TCGA-BR-6452 TCGA-BR-6455 TCGA-BR-6457 TCGA-BR-6563 
        5.62         0.10         0.95         1.41         1.35         0.85 
TCGA-BR-6564 TCGA-BR-6566 TCGA-BR-6705 TCGA-BR-6706 TCGA-BR-6707 TCGA-BR-6709 
        0.82         0.62         1.71         2.17         0.99         1.22 
TCGA-BR-6710 TCGA-BR-6801 TCGA-BR-6802 TCGA-BR-6803 TCGA-BR-6852 TCGA-BR-7196 
        0.66         1.12         0.76         0.66         0.26         1.22 
TCGA-BR-7197 TCGA-BR-7703 TCGA-BR-7704 TCGA-BR-7707 TCGA-BR-7715 TCGA-BR-7716 
        1.48         0.46         1.25         0.13         1.05         0.82 
TCGA-BR-7717 TCGA-BR-7722 TCGA-BR-7851 TCGA-BR-7901 TCGA-BR-7957 TCGA-BR-7958 
        0.69         0.16         0.99         0.95         0.69         0.16 
TCGA-BR-7959 TCGA-BR-8059 TCGA-BR-8077 TCGA-BR-8078 TCGA-BR-8080 TCGA-BR-8081 
        1.08         0.82         0.69         0.95         0.49         0.46 
TCGA-BR-8284 TCGA-BR-8285 TCGA-BR-8286 TCGA-BR-8289 TCGA-BR-8291 TCGA-BR-8296 
        0.72         0.26         0.43         0.26         1.18         1.48 
TCGA-BR-8297 TCGA-BR-8592 TCGA-BR-A4IU TCGA-BR-A4IV TCGA-BR-A4IY TCGA-BR-A4IZ 
        0.76         0.20         0.59         0.92         0.39         0.79 
TCGA-BR-A4J2 TCGA-BR-A4J4 TCGA-BR-A4J5 TCGA-BR-A4J6 TCGA-BR-A4J8 TCGA-BR-A4J9 
        0.79         0.53         0.43         0.13         0.23         0.10 
TCGA-BR-A4PF TCGA-BR-A4QI TCGA-BR-A4QL TCGA-CD-5798 TCGA-CD-5799 TCGA-CD-5800 
        0.72         0.49         2.24         0.82         0.69         0.36 
TCGA-CD-5801 TCGA-CD-5802 TCGA-CD-5803 TCGA-CG-4300 TCGA-CG-4301 TCGA-CG-4304 
        0.49         0.30         0.07        20.02         3.02        27.02 
TCGA-CG-4305 TCGA-CG-4306 TCGA-CG-4437 TCGA-CG-4441 TCGA-CG-4444 TCGA-CG-4449 
       15.95         1.02         8.05        14.01        47.05        19.07 
TCGA-CG-4455 TCGA-CG-4460 TCGA-CG-4462 TCGA-CG-4465 TCGA-CG-4469 TCGA-CG-4472 
       12.03        21.99         1.02         8.98         7.07        12.00 
TCGA-CG-4474 TCGA-CG-4477 TCGA-CG-5716 TCGA-CG-5717 TCGA-CG-5718 TCGA-CG-5719 
        1.02         1.02         1.02         6.94         1.02         1.02 
TCGA-CG-5720 TCGA-CG-5721 TCGA-CG-5722 TCGA-CG-5723 TCGA-CG-5724 TCGA-CG-5726 
        0.99         5.98         0.95        70.06        12.03        28.96 
TCGA-CG-5727 TCGA-CG-5728 TCGA-CG-5730 TCGA-CG-5733 TCGA-CG-5734 TCGA-D7-5577 
       31.04        65.10         4.01        21.07         7.99         8.65 
TCGA-D7-5578 TCGA-D7-5579 TCGA-D7-6518 TCGA-D7-6519 TCGA-D7-6521 TCGA-D7-6522 
        3.58         4.54         9.80        15.65         8.19         6.90 
TCGA-D7-6524 TCGA-D7-6526 TCGA-D7-6527 TCGA-D7-6528 TCGA-D7-6815 TCGA-D7-6817 
        0.69         6.61         4.14         1.68         3.65         4.70 
TCGA-D7-6818 TCGA-D7-6822 TCGA-EQ-8122 TCGA-F1-6177 TCGA-F1-6874 TCGA-F1-6875 
        4.04         4.27         7.79         6.54         2.01        72.23 
TCGA-FP-7735 TCGA-FP-7829 TCGA-FP-7916 TCGA-FP-7998 TCGA-FP-8099 TCGA-FP-8209 
        0.39         0.20         3.02         3.58         1.02        59.05 
TCGA-FP-8210 TCGA-HJ-7597 TCGA-IN-7806 TCGA-IN-7808 TCGA-IP-7968 
        5.03        26.43         6.87         3.55         2.53 

      19P LOSS CNV 19P LOSS WILD-TYPE 
              0.56               0.07 
      19P LOSS CNV 19P LOSS WILD-TYPE 
             55.04              72.23 
      19P LOSS CNV 19P LOSS WILD-TYPE 
             4.275              1.080 
[1] "0.6 - 55.0 (4.3)" "0.1 - 72.2 (1.1)"
        TCGA-B7-5816         TCGA-B7-5818         TCGA-BR-6452 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-BR-6455         TCGA-BR-6457         TCGA-BR-6458 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE"       "19P LOSS CNV" 
        TCGA-BR-6563         TCGA-BR-6564         TCGA-BR-6565 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE"       "19P LOSS CNV" 
        TCGA-BR-6566         TCGA-BR-6705         TCGA-BR-6706 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-BR-6707         TCGA-BR-6709         TCGA-BR-6710 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-BR-6801         TCGA-BR-6802         TCGA-BR-6803 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-BR-6852         TCGA-BR-7196         TCGA-BR-7197 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-BR-7703         TCGA-BR-7704         TCGA-BR-7707 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-BR-7715         TCGA-BR-7716         TCGA-BR-7717 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-BR-7722         TCGA-BR-7723         TCGA-BR-7851 
"19P LOSS WILD-TYPE"       "19P LOSS CNV" "19P LOSS WILD-TYPE" 
        TCGA-BR-7901         TCGA-BR-7957         TCGA-BR-7958 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-BR-7959         TCGA-BR-8059         TCGA-BR-8060 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE"       "19P LOSS CNV" 
        TCGA-BR-8077         TCGA-BR-8078         TCGA-BR-8080 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-BR-8081         TCGA-BR-8284         TCGA-BR-8285 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-BR-8286         TCGA-BR-8289         TCGA-BR-8291 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-BR-8295         TCGA-BR-8296         TCGA-BR-8297 
      "19P LOSS CNV" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-BR-8592         TCGA-BR-A4IU         TCGA-BR-A4IV 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-BR-A4IY         TCGA-BR-A4IZ         TCGA-BR-A4J1 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE"       "19P LOSS CNV" 
        TCGA-BR-A4J2         TCGA-BR-A4J4         TCGA-BR-A4J5 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-BR-A4J6         TCGA-BR-A4J8         TCGA-BR-A4J9 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-BR-A4PF         TCGA-BR-A4QI         TCGA-BR-A4QL 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-CD-5798         TCGA-CD-5799         TCGA-CD-5800 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-CD-5801         TCGA-CD-5802         TCGA-CD-5803 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-CG-4300         TCGA-CG-4301         TCGA-CG-4304 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-CG-4305         TCGA-CG-4306         TCGA-CG-4436 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE"       "19P LOSS CNV" 
        TCGA-CG-4437         TCGA-CG-4438         TCGA-CG-4440 
"19P LOSS WILD-TYPE"       "19P LOSS CNV"       "19P LOSS CNV" 
        TCGA-CG-4441         TCGA-CG-4443         TCGA-CG-4444 
"19P LOSS WILD-TYPE"       "19P LOSS CNV" "19P LOSS WILD-TYPE" 
        TCGA-CG-4449         TCGA-CG-4455         TCGA-CG-4460 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-CG-4462         TCGA-CG-4465         TCGA-CG-4466 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE"       "19P LOSS CNV" 
        TCGA-CG-4469         TCGA-CG-4472         TCGA-CG-4474 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-CG-4477         TCGA-CG-5716         TCGA-CG-5717 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-CG-5718         TCGA-CG-5719         TCGA-CG-5720 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-CG-5721         TCGA-CG-5722         TCGA-CG-5723 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-CG-5724         TCGA-CG-5725         TCGA-CG-5726 
"19P LOSS WILD-TYPE"       "19P LOSS CNV" "19P LOSS WILD-TYPE" 
        TCGA-CG-5727         TCGA-CG-5728         TCGA-CG-5730 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-CG-5732         TCGA-CG-5733         TCGA-CG-5734 
      "19P LOSS CNV" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-D7-5577         TCGA-D7-5578         TCGA-D7-5579 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-D7-6518         TCGA-D7-6519         TCGA-D7-6520 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE"       "19P LOSS CNV" 
        TCGA-D7-6521         TCGA-D7-6522         TCGA-D7-6524 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-D7-6525         TCGA-D7-6526         TCGA-D7-6527 
      "19P LOSS CNV" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-D7-6528         TCGA-D7-6815         TCGA-D7-6817 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-D7-6818         TCGA-D7-6820         TCGA-D7-6822 
"19P LOSS WILD-TYPE"       "19P LOSS CNV" "19P LOSS WILD-TYPE" 
        TCGA-EQ-5647         TCGA-EQ-8122         TCGA-F1-6177 
      "19P LOSS CNV" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-F1-6874         TCGA-F1-6875         TCGA-FP-7735 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-FP-7829         TCGA-FP-7916         TCGA-FP-7998 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-FP-8099         TCGA-FP-8209         TCGA-FP-8210 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-FP-8631         TCGA-HJ-7597         TCGA-IN-7806 
      "19P LOSS CNV" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-IN-7808         TCGA-IP-7968 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-B7-5816         TCGA-B7-5818         TCGA-BR-6452 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-BR-6455         TCGA-BR-6457         TCGA-BR-6458 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE"       "19P LOSS CNV" 
        TCGA-BR-6563         TCGA-BR-6564         TCGA-BR-6565 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE"       "19P LOSS CNV" 
        TCGA-BR-6566         TCGA-BR-6705         TCGA-BR-6706 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-BR-6707         TCGA-BR-6709         TCGA-BR-6710 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-BR-6801         TCGA-BR-6802         TCGA-BR-6803 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-BR-6852         TCGA-BR-7196         TCGA-BR-7197 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-BR-7703         TCGA-BR-7704         TCGA-BR-7707 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-BR-7715         TCGA-BR-7716         TCGA-BR-7717 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-BR-7722         TCGA-BR-7723         TCGA-BR-7851 
"19P LOSS WILD-TYPE"       "19P LOSS CNV" "19P LOSS WILD-TYPE" 
        TCGA-BR-7901         TCGA-BR-7957         TCGA-BR-7958 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-BR-7959         TCGA-BR-8059         TCGA-BR-8060 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE"       "19P LOSS CNV" 
        TCGA-BR-8077         TCGA-BR-8078         TCGA-BR-8080 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-BR-8081         TCGA-BR-8284         TCGA-BR-8285 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-BR-8286         TCGA-BR-8289         TCGA-BR-8291 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-BR-8295         TCGA-BR-8296         TCGA-BR-8297 
      "19P LOSS CNV" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-BR-8592         TCGA-BR-A4IU         TCGA-BR-A4IV 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-BR-A4IY         TCGA-BR-A4IZ         TCGA-BR-A4J1 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE"       "19P LOSS CNV" 
        TCGA-BR-A4J2         TCGA-BR-A4J4         TCGA-BR-A4J5 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-BR-A4J6         TCGA-BR-A4J8         TCGA-BR-A4J9 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-BR-A4PF         TCGA-BR-A4QI         TCGA-BR-A4QL 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-CD-5798         TCGA-CD-5799         TCGA-CD-5800 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-CD-5801         TCGA-CD-5802         TCGA-CD-5803 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-CG-4300         TCGA-CG-4301         TCGA-CG-4304 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-CG-4305         TCGA-CG-4306         TCGA-CG-4436 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE"       "19P LOSS CNV" 
        TCGA-CG-4437         TCGA-CG-4438         TCGA-CG-4440 
"19P LOSS WILD-TYPE"       "19P LOSS CNV"       "19P LOSS CNV" 
        TCGA-CG-4441         TCGA-CG-4443         TCGA-CG-4444 
"19P LOSS WILD-TYPE"       "19P LOSS CNV" "19P LOSS WILD-TYPE" 
        TCGA-CG-4449         TCGA-CG-4455         TCGA-CG-4460 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-CG-4462         TCGA-CG-4465         TCGA-CG-4466 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE"       "19P LOSS CNV" 
        TCGA-CG-4469         TCGA-CG-4472         TCGA-CG-4474 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-CG-4477         TCGA-CG-5716         TCGA-CG-5717 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-CG-5718         TCGA-CG-5719         TCGA-CG-5720 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-CG-5721         TCGA-CG-5722         TCGA-CG-5723 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-CG-5724         TCGA-CG-5725         TCGA-CG-5726 
"19P LOSS WILD-TYPE"       "19P LOSS CNV" "19P LOSS WILD-TYPE" 
        TCGA-CG-5727         TCGA-CG-5728         TCGA-CG-5730 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-CG-5732         TCGA-CG-5733         TCGA-CG-5734 
      "19P LOSS CNV" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-D7-5577         TCGA-D7-5578         TCGA-D7-5579 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-D7-6518         TCGA-D7-6519         TCGA-D7-6520 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE"       "19P LOSS CNV" 
        TCGA-D7-6521         TCGA-D7-6522         TCGA-D7-6524 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-D7-6525         TCGA-D7-6526         TCGA-D7-6527 
      "19P LOSS CNV" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-D7-6528         TCGA-D7-6815         TCGA-D7-6817 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-D7-6818         TCGA-D7-6820         TCGA-D7-6822 
"19P LOSS WILD-TYPE"       "19P LOSS CNV" "19P LOSS WILD-TYPE" 
        TCGA-EQ-5647         TCGA-EQ-8122         TCGA-F1-6177 
      "19P LOSS CNV" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-F1-6874         TCGA-F1-6875         TCGA-FP-7735 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-FP-7829         TCGA-FP-7916         TCGA-FP-7998 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-FP-8099         TCGA-FP-8209         TCGA-FP-8210 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-FP-8631         TCGA-HJ-7597         TCGA-IN-7806 
      "19P LOSS CNV" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-IN-7808         TCGA-IP-7968 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-B7-5816         TCGA-B7-5818         TCGA-BR-6452 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-BR-6455         TCGA-BR-6457         TCGA-BR-6458 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE"       "19P LOSS CNV" 
        TCGA-BR-6563         TCGA-BR-6564         TCGA-BR-6565 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE"       "19P LOSS CNV" 
        TCGA-BR-6566         TCGA-BR-6705         TCGA-BR-6706 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-BR-6707         TCGA-BR-6709         TCGA-BR-6710 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-BR-6801         TCGA-BR-6802         TCGA-BR-6803 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-BR-6852         TCGA-BR-7196         TCGA-BR-7197 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-BR-7703         TCGA-BR-7704         TCGA-BR-7707 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-BR-7715         TCGA-BR-7716         TCGA-BR-7717 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-BR-7722         TCGA-BR-7723         TCGA-BR-7851 
"19P LOSS WILD-TYPE"       "19P LOSS CNV" "19P LOSS WILD-TYPE" 
        TCGA-BR-7901         TCGA-BR-7957         TCGA-BR-7958 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-BR-7959         TCGA-BR-8059         TCGA-BR-8060 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE"       "19P LOSS CNV" 
        TCGA-BR-8077         TCGA-BR-8078         TCGA-BR-8080 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-BR-8081         TCGA-BR-8284         TCGA-BR-8285 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-BR-8286         TCGA-BR-8289         TCGA-BR-8291 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-BR-8295         TCGA-BR-8296         TCGA-BR-8297 
      "19P LOSS CNV" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-BR-8592         TCGA-BR-A4IU         TCGA-BR-A4IV 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-BR-A4IY         TCGA-BR-A4IZ         TCGA-BR-A4J1 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE"       "19P LOSS CNV" 
        TCGA-BR-A4J2         TCGA-BR-A4J4         TCGA-BR-A4J5 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-BR-A4J6         TCGA-BR-A4J8         TCGA-BR-A4J9 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-BR-A4PF         TCGA-BR-A4QI         TCGA-BR-A4QL 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-CD-5798         TCGA-CD-5799         TCGA-CD-5800 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-CD-5801         TCGA-CD-5802         TCGA-CD-5803 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-CG-4300         TCGA-CG-4301         TCGA-CG-4304 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-CG-4305         TCGA-CG-4306         TCGA-CG-4436 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE"       "19P LOSS CNV" 
        TCGA-CG-4437         TCGA-CG-4438         TCGA-CG-4440 
"19P LOSS WILD-TYPE"       "19P LOSS CNV"       "19P LOSS CNV" 
        TCGA-CG-4441         TCGA-CG-4443         TCGA-CG-4444 
"19P LOSS WILD-TYPE"       "19P LOSS CNV" "19P LOSS WILD-TYPE" 
        TCGA-CG-4449         TCGA-CG-4455         TCGA-CG-4460 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-CG-4462         TCGA-CG-4465         TCGA-CG-4466 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE"       "19P LOSS CNV" 
        TCGA-CG-4469         TCGA-CG-4472         TCGA-CG-4474 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-CG-4477         TCGA-CG-5716         TCGA-CG-5717 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-CG-5718         TCGA-CG-5719         TCGA-CG-5720 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-CG-5721         TCGA-CG-5722         TCGA-CG-5723 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-CG-5724         TCGA-CG-5725         TCGA-CG-5726 
"19P LOSS WILD-TYPE"       "19P LOSS CNV" "19P LOSS WILD-TYPE" 
        TCGA-CG-5727         TCGA-CG-5728         TCGA-CG-5730 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-CG-5732         TCGA-CG-5733         TCGA-CG-5734 
      "19P LOSS CNV" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-D7-5577         TCGA-D7-5578         TCGA-D7-5579 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-D7-6518         TCGA-D7-6519         TCGA-D7-6520 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE"       "19P LOSS CNV" 
        TCGA-D7-6521         TCGA-D7-6522         TCGA-D7-6524 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-D7-6525         TCGA-D7-6526         TCGA-D7-6527 
      "19P LOSS CNV" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-D7-6528         TCGA-D7-6815         TCGA-D7-6817 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-D7-6818         TCGA-D7-6820         TCGA-D7-6822 
"19P LOSS WILD-TYPE"       "19P LOSS CNV" "19P LOSS WILD-TYPE" 
        TCGA-EQ-5647         TCGA-EQ-8122         TCGA-F1-6177 
      "19P LOSS CNV" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-F1-6874         TCGA-F1-6875         TCGA-FP-7735 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-FP-7829         TCGA-FP-7916         TCGA-FP-7998 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-FP-8099         TCGA-FP-8209         TCGA-FP-8210 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-FP-8631         TCGA-HJ-7597         TCGA-IN-7806 
      "19P LOSS CNV" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-IN-7808         TCGA-IP-7968 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
[1] "hr=" "1"  
D69V2, continuous
D69V3, binary
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  19P LOSS CNV          6   14
  19P LOSS WILD-TYPE   66   94
        clus
vv       19P LOSS CNV 19P LOSS WILD-TYPE
  FEMALE            6                 66
  MALE             14                 94
                    vv
clus                 STOMACH  ADENOCARCINOMA  DIFFUSE TYPE
  19P LOSS CNV                                           0
  19P LOSS WILD-TYPE                                    10
                    vv
clus                 STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  19P LOSS CNV                                                            3
  19P LOSS WILD-TYPE                                                     13
                    vv
clus                 STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  19P LOSS CNV                                                                       1
  19P LOSS WILD-TYPE                                                                 7
                    vv
clus                 STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE
  19P LOSS CNV                                                              0
  19P LOSS WILD-TYPE                                                        3
                    vv
clus                 STOMACH ADENOCARCINOMA  SIGNET RING TYPE
  19P LOSS CNV                                              0
  19P LOSS WILD-TYPE                                        1
                    vv
clus                 STOMACH ADENOCARCINOMA - DIFFUSE TYPE
  19P LOSS CNV                                           1
  19P LOSS WILD-TYPE                                    15
                    vv
clus                 STOMACH ADENOCARCINOMA - NOT OTHERWISE SPECIFIED (NOS)
  19P LOSS CNV                                                            7
  19P LOSS WILD-TYPE                                                     66
                    vv
clus                 STOMACH INTESTINAL ADENOCARCINOMA - MUCINOUS TYPE
  19P LOSS CNV                                                       0
  19P LOSS WILD-TYPE                                                 7
                    vv
clus                 STOMACH INTESTINAL ADENOCARCINOMA - PAPILLARY TYPE
  19P LOSS CNV                                                        0
  19P LOSS WILD-TYPE                                                  3
                    vv
clus                 STOMACH INTESTINAL ADENOCARCINOMA - TUBULAR TYPE
  19P LOSS CNV                                                      2
  19P LOSS WILD-TYPE                                                8
                    vv
clus                 STOMACH INTESTINAL ADENOCARCINOMA - TYPE NOT OTHERWISE SPECIFIED (NOS)
  19P LOSS CNV                                                                            6
  19P LOSS WILD-TYPE                                                                     22
D69V4, multiclass
                    vv
clus                 T1 T2 T3 T4
  19P LOSS CNV        1  7  5  2
  19P LOSS WILD-TYPE  5 45 51 16
D69V5, multiclass
    clus
vv   19P LOSS CNV 19P LOSS WILD-TYPE
  T1            1                  5
  T2            7                 45
  T3            5                 51
  T4            2                 16
                    vv
clus                 N0 N1 N2 N3
  19P LOSS CNV        5  3  4  3
  19P LOSS WILD-TYPE 39 46 19 12
D69V6, multiclass
    clus
vv   19P LOSS CNV 19P LOSS WILD-TYPE
  N0            5                 39
  N1            3                 46
  N2            4                 19
  N3            3                 12
                    vv
clus                  M0  M1  MX
  19P LOSS CNV        14   2   0
  19P LOSS WILD-TYPE 104  14   8
D69V7, multiclass
    clus
vv   19P LOSS CNV 19P LOSS WILD-TYPE
  M0           14                104
  M1            2                 14
  MX            0                  8
                    vv
clus                  I II III IV
  19P LOSS CNV        4  4   3  4
  19P LOSS WILD-TYPE 20 33  36 22
D69V8, multiclass
     clus
vv    19P LOSS CNV 19P LOSS WILD-TYPE
  I              4                 20
  II             4                 33
  III            3                 36
  IV             4                 22
D69V9, binary
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  19P LOSS CNV          0   20
  19P LOSS WILD-TYPE    5  155
     clus
vv    19P LOSS CNV 19P LOSS WILD-TYPE
  NO             0                  5
  YES           20                155
                    vv
clus                  R0  R1  R2  RX
  19P LOSS CNV        17   0   2   1
  19P LOSS WILD-TYPE 108   7  10  24
D69V10, multiclass
    clus
vv   19P LOSS CNV 19P LOSS WILD-TYPE
  R0           17                108
  R1            0                  7
  R2            2                 10
  RX            1                 24
D69V11, continuous

Clustering(70) Variable = 19q loss
D70V1, survival
                    sevent
clus2                  0   1
  19Q LOSS CNV         9   3
  19Q LOSS WILD-TYPE 115  16
      19Q LOSS CNV 19Q LOSS WILD-TYPE 
                12                131 
      19Q LOSS CNV 19Q LOSS WILD-TYPE 
                 3                 16 
$`19Q LOSS CNV`
TCGA-BR-6565 TCGA-BR-7723 TCGA-BR-8060 TCGA-CG-4436 TCGA-CG-4440 TCGA-CG-4443 
        0.62         4.54         1.32        52.96         4.01        29.98 
TCGA-CG-4466 TCGA-CG-5725 TCGA-CG-5732 TCGA-D7-6820 TCGA-EQ-5647 TCGA-FP-8631 
       18.94        15.02        55.04         2.93         0.62         0.56 

$`19Q LOSS WILD-TYPE`
TCGA-B7-5816 TCGA-B7-5818 TCGA-BR-6452 TCGA-BR-6455 TCGA-BR-6457 TCGA-BR-6458 
        5.62         0.10         0.95         1.41         1.35         1.35 
TCGA-BR-6563 TCGA-BR-6564 TCGA-BR-6566 TCGA-BR-6705 TCGA-BR-6706 TCGA-BR-6707 
        0.85         0.82         0.62         1.71         2.17         0.99 
TCGA-BR-6709 TCGA-BR-6710 TCGA-BR-6801 TCGA-BR-6802 TCGA-BR-6803 TCGA-BR-6852 
        1.22         0.66         1.12         0.76         0.66         0.26 
TCGA-BR-7196 TCGA-BR-7197 TCGA-BR-7703 TCGA-BR-7704 TCGA-BR-7707 TCGA-BR-7715 
        1.22         1.48         0.46         1.25         0.13         1.05 
TCGA-BR-7716 TCGA-BR-7717 TCGA-BR-7722 TCGA-BR-7851 TCGA-BR-7901 TCGA-BR-7957 
        0.82         0.69         0.16         0.99         0.95         0.69 
TCGA-BR-7958 TCGA-BR-7959 TCGA-BR-8059 TCGA-BR-8077 TCGA-BR-8078 TCGA-BR-8080 
        0.16         1.08         0.82         0.69         0.95         0.49 
TCGA-BR-8081 TCGA-BR-8284 TCGA-BR-8285 TCGA-BR-8286 TCGA-BR-8289 TCGA-BR-8291 
        0.46         0.72         0.26         0.43         0.26         1.18 
TCGA-BR-8295 TCGA-BR-8296 TCGA-BR-8297 TCGA-BR-8592 TCGA-BR-A4IU TCGA-BR-A4IV 
        1.55         1.48         0.76         0.20         0.59         0.92 
TCGA-BR-A4IY TCGA-BR-A4IZ TCGA-BR-A4J1 TCGA-BR-A4J2 TCGA-BR-A4J4 TCGA-BR-A4J5 
        0.39         0.79         0.72         0.79         0.53         0.43 
TCGA-BR-A4J6 TCGA-BR-A4J8 TCGA-BR-A4J9 TCGA-BR-A4PF TCGA-BR-A4QI TCGA-BR-A4QL 
        0.13         0.23         0.10         0.72         0.49         2.24 
TCGA-CD-5798 TCGA-CD-5799 TCGA-CD-5800 TCGA-CD-5801 TCGA-CD-5802 TCGA-CD-5803 
        0.82         0.69         0.36         0.49         0.30         0.07 
TCGA-CG-4300 TCGA-CG-4301 TCGA-CG-4304 TCGA-CG-4305 TCGA-CG-4306 TCGA-CG-4437 
       20.02         3.02        27.02        15.95         1.02         8.05 
TCGA-CG-4438 TCGA-CG-4441 TCGA-CG-4444 TCGA-CG-4449 TCGA-CG-4455 TCGA-CG-4460 
       54.05        14.01        47.05        19.07        12.03        21.99 
TCGA-CG-4462 TCGA-CG-4465 TCGA-CG-4469 TCGA-CG-4472 TCGA-CG-4474 TCGA-CG-4477 
        1.02         8.98         7.07        12.00         1.02         1.02 
TCGA-CG-5716 TCGA-CG-5717 TCGA-CG-5718 TCGA-CG-5719 TCGA-CG-5720 TCGA-CG-5721 
        1.02         6.94         1.02         1.02         0.99         5.98 
TCGA-CG-5722 TCGA-CG-5723 TCGA-CG-5724 TCGA-CG-5726 TCGA-CG-5727 TCGA-CG-5728 
        0.95        70.06        12.03        28.96        31.04        65.10 
TCGA-CG-5730 TCGA-CG-5733 TCGA-CG-5734 TCGA-D7-5577 TCGA-D7-5578 TCGA-D7-5579 
        4.01        21.07         7.99         8.65         3.58         4.54 
TCGA-D7-6518 TCGA-D7-6519 TCGA-D7-6520 TCGA-D7-6521 TCGA-D7-6522 TCGA-D7-6524 
        9.80        15.65         9.63         8.19         6.90         0.69 
TCGA-D7-6525 TCGA-D7-6526 TCGA-D7-6527 TCGA-D7-6528 TCGA-D7-6815 TCGA-D7-6817 
        5.95         6.61         4.14         1.68         3.65         4.70 
TCGA-D7-6818 TCGA-D7-6822 TCGA-EQ-8122 TCGA-F1-6177 TCGA-F1-6874 TCGA-F1-6875 
        4.04         4.27         7.79         6.54         2.01        72.23 
TCGA-FP-7735 TCGA-FP-7829 TCGA-FP-7916 TCGA-FP-7998 TCGA-FP-8099 TCGA-FP-8209 
        0.39         0.20         3.02         3.58         1.02        59.05 
TCGA-FP-8210 TCGA-HJ-7597 TCGA-IN-7806 TCGA-IN-7808 TCGA-IP-7968 
        5.03        26.43         6.87         3.55         2.53 

      19Q LOSS CNV 19Q LOSS WILD-TYPE 
              0.56               0.07 
      19Q LOSS CNV 19Q LOSS WILD-TYPE 
             55.04              72.23 
      19Q LOSS CNV 19Q LOSS WILD-TYPE 
             4.275              1.180 
[1] "0.6 - 55.0 (4.3)" "0.1 - 72.2 (1.2)"
        TCGA-B7-5816         TCGA-B7-5818         TCGA-BR-6452 
"19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" 
        TCGA-BR-6455         TCGA-BR-6457         TCGA-BR-6458 
"19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" 
        TCGA-BR-6563         TCGA-BR-6564         TCGA-BR-6565 
"19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE"       "19Q LOSS CNV" 
        TCGA-BR-6566         TCGA-BR-6705         TCGA-BR-6706 
"19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" 
        TCGA-BR-6707         TCGA-BR-6709         TCGA-BR-6710 
"19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" 
        TCGA-BR-6801         TCGA-BR-6802         TCGA-BR-6803 
"19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" 
        TCGA-BR-6852         TCGA-BR-7196         TCGA-BR-7197 
"19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" 
        TCGA-BR-7703         TCGA-BR-7704         TCGA-BR-7707 
"19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" 
        TCGA-BR-7715         TCGA-BR-7716         TCGA-BR-7717 
"19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" 
        TCGA-BR-7722         TCGA-BR-7723         TCGA-BR-7851 
"19Q LOSS WILD-TYPE"       "19Q LOSS CNV" "19Q LOSS WILD-TYPE" 
        TCGA-BR-7901         TCGA-BR-7957         TCGA-BR-7958 
"19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" 
        TCGA-BR-7959         TCGA-BR-8059         TCGA-BR-8060 
"19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE"       "19Q LOSS CNV" 
        TCGA-BR-8077         TCGA-BR-8078         TCGA-BR-8080 
"19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" 
        TCGA-BR-8081         TCGA-BR-8284         TCGA-BR-8285 
"19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" 
        TCGA-BR-8286         TCGA-BR-8289         TCGA-BR-8291 
"19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" 
        TCGA-BR-8295         TCGA-BR-8296         TCGA-BR-8297 
"19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" 
        TCGA-BR-8592         TCGA-BR-A4IU         TCGA-BR-A4IV 
"19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" 
        TCGA-BR-A4IY         TCGA-BR-A4IZ         TCGA-BR-A4J1 
"19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" 
        TCGA-BR-A4J2         TCGA-BR-A4J4         TCGA-BR-A4J5 
"19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" 
        TCGA-BR-A4J6         TCGA-BR-A4J8         TCGA-BR-A4J9 
"19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" 
        TCGA-BR-A4PF         TCGA-BR-A4QI         TCGA-BR-A4QL 
"19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" 
        TCGA-CD-5798         TCGA-CD-5799         TCGA-CD-5800 
"19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" 
        TCGA-CD-5801         TCGA-CD-5802         TCGA-CD-5803 
"19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" 
        TCGA-CG-4300         TCGA-CG-4301         TCGA-CG-4304 
"19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" 
        TCGA-CG-4305         TCGA-CG-4306         TCGA-CG-4436 
"19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE"       "19Q LOSS CNV" 
        TCGA-CG-4437         TCGA-CG-4438         TCGA-CG-4440 
"19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE"       "19Q LOSS CNV" 
        TCGA-CG-4441         TCGA-CG-4443         TCGA-CG-4444 
"19Q LOSS WILD-TYPE"       "19Q LOSS CNV" "19Q LOSS WILD-TYPE" 
        TCGA-CG-4449         TCGA-CG-4455         TCGA-CG-4460 
"19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" 
        TCGA-CG-4462         TCGA-CG-4465         TCGA-CG-4466 
"19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE"       "19Q LOSS CNV" 
        TCGA-CG-4469         TCGA-CG-4472         TCGA-CG-4474 
"19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" 
        TCGA-CG-4477         TCGA-CG-5716         TCGA-CG-5717 
"19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" 
        TCGA-CG-5718         TCGA-CG-5719         TCGA-CG-5720 
"19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" 
        TCGA-CG-5721         TCGA-CG-5722         TCGA-CG-5723 
"19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" 
        TCGA-CG-5724         TCGA-CG-5725         TCGA-CG-5726 
"19Q LOSS WILD-TYPE"       "19Q LOSS CNV" "19Q LOSS WILD-TYPE" 
        TCGA-CG-5727         TCGA-CG-5728         TCGA-CG-5730 
"19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" 
        TCGA-CG-5732         TCGA-CG-5733         TCGA-CG-5734 
      "19Q LOSS CNV" "19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" 
        TCGA-D7-5577         TCGA-D7-5578         TCGA-D7-5579 
"19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" 
        TCGA-D7-6518         TCGA-D7-6519         TCGA-D7-6520 
"19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" 
        TCGA-D7-6521         TCGA-D7-6522         TCGA-D7-6524 
"19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" 
        TCGA-D7-6525         TCGA-D7-6526         TCGA-D7-6527 
"19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" 
        TCGA-D7-6528         TCGA-D7-6815         TCGA-D7-6817 
"19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" 
        TCGA-D7-6818         TCGA-D7-6820         TCGA-D7-6822 
"19Q LOSS WILD-TYPE"       "19Q LOSS CNV" "19Q LOSS WILD-TYPE" 
        TCGA-EQ-5647         TCGA-EQ-8122         TCGA-F1-6177 
      "19Q LOSS CNV" "19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" 
        TCGA-F1-6874         TCGA-F1-6875         TCGA-FP-7735 
"19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" 
        TCGA-FP-7829         TCGA-FP-7916         TCGA-FP-7998 
"19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" 
        TCGA-FP-8099         TCGA-FP-8209         TCGA-FP-8210 
"19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" 
        TCGA-FP-8631         TCGA-HJ-7597         TCGA-IN-7806 
      "19Q LOSS CNV" "19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" 
        TCGA-IN-7808         TCGA-IP-7968 
"19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" 
        TCGA-B7-5816         TCGA-B7-5818         TCGA-BR-6452 
"19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" 
        TCGA-BR-6455         TCGA-BR-6457         TCGA-BR-6458 
"19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" 
        TCGA-BR-6563         TCGA-BR-6564         TCGA-BR-6565 
"19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE"       "19Q LOSS CNV" 
        TCGA-BR-6566         TCGA-BR-6705         TCGA-BR-6706 
"19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" 
        TCGA-BR-6707         TCGA-BR-6709         TCGA-BR-6710 
"19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" 
        TCGA-BR-6801         TCGA-BR-6802         TCGA-BR-6803 
"19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" 
        TCGA-BR-6852         TCGA-BR-7196         TCGA-BR-7197 
"19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" 
        TCGA-BR-7703         TCGA-BR-7704         TCGA-BR-7707 
"19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" 
        TCGA-BR-7715         TCGA-BR-7716         TCGA-BR-7717 
"19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" 
        TCGA-BR-7722         TCGA-BR-7723         TCGA-BR-7851 
"19Q LOSS WILD-TYPE"       "19Q LOSS CNV" "19Q LOSS WILD-TYPE" 
        TCGA-BR-7901         TCGA-BR-7957         TCGA-BR-7958 
"19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" 
        TCGA-BR-7959         TCGA-BR-8059         TCGA-BR-8060 
"19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE"       "19Q LOSS CNV" 
        TCGA-BR-8077         TCGA-BR-8078         TCGA-BR-8080 
"19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" 
        TCGA-BR-8081         TCGA-BR-8284         TCGA-BR-8285 
"19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" 
        TCGA-BR-8286         TCGA-BR-8289         TCGA-BR-8291 
"19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" 
        TCGA-BR-8295         TCGA-BR-8296         TCGA-BR-8297 
"19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" 
        TCGA-BR-8592         TCGA-BR-A4IU         TCGA-BR-A4IV 
"19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" 
        TCGA-BR-A4IY         TCGA-BR-A4IZ         TCGA-BR-A4J1 
"19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" 
        TCGA-BR-A4J2         TCGA-BR-A4J4         TCGA-BR-A4J5 
"19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" 
        TCGA-BR-A4J6         TCGA-BR-A4J8         TCGA-BR-A4J9 
"19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" 
        TCGA-BR-A4PF         TCGA-BR-A4QI         TCGA-BR-A4QL 
"19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" 
        TCGA-CD-5798         TCGA-CD-5799         TCGA-CD-5800 
"19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" 
        TCGA-CD-5801         TCGA-CD-5802         TCGA-CD-5803 
"19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" 
        TCGA-CG-4300         TCGA-CG-4301         TCGA-CG-4304 
"19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" 
        TCGA-CG-4305         TCGA-CG-4306         TCGA-CG-4436 
"19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE"       "19Q LOSS CNV" 
        TCGA-CG-4437         TCGA-CG-4438         TCGA-CG-4440 
"19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE"       "19Q LOSS CNV" 
        TCGA-CG-4441         TCGA-CG-4443         TCGA-CG-4444 
"19Q LOSS WILD-TYPE"       "19Q LOSS CNV" "19Q LOSS WILD-TYPE" 
        TCGA-CG-4449         TCGA-CG-4455         TCGA-CG-4460 
"19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" 
        TCGA-CG-4462         TCGA-CG-4465         TCGA-CG-4466 
"19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE"       "19Q LOSS CNV" 
        TCGA-CG-4469         TCGA-CG-4472         TCGA-CG-4474 
"19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" 
        TCGA-CG-4477         TCGA-CG-5716         TCGA-CG-5717 
"19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" 
        TCGA-CG-5718         TCGA-CG-5719         TCGA-CG-5720 
"19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" 
        TCGA-CG-5721         TCGA-CG-5722         TCGA-CG-5723 
"19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" 
        TCGA-CG-5724         TCGA-CG-5725         TCGA-CG-5726 
"19Q LOSS WILD-TYPE"       "19Q LOSS CNV" "19Q LOSS WILD-TYPE" 
        TCGA-CG-5727         TCGA-CG-5728         TCGA-CG-5730 
"19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" 
        TCGA-CG-5732         TCGA-CG-5733         TCGA-CG-5734 
      "19Q LOSS CNV" "19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" 
        TCGA-D7-5577         TCGA-D7-5578         TCGA-D7-5579 
"19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" 
        TCGA-D7-6518         TCGA-D7-6519         TCGA-D7-6520 
"19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" 
        TCGA-D7-6521         TCGA-D7-6522         TCGA-D7-6524 
"19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" 
        TCGA-D7-6525         TCGA-D7-6526         TCGA-D7-6527 
"19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" 
        TCGA-D7-6528         TCGA-D7-6815         TCGA-D7-6817 
"19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" 
        TCGA-D7-6818         TCGA-D7-6820         TCGA-D7-6822 
"19Q LOSS WILD-TYPE"       "19Q LOSS CNV" "19Q LOSS WILD-TYPE" 
        TCGA-EQ-5647         TCGA-EQ-8122         TCGA-F1-6177 
      "19Q LOSS CNV" "19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" 
        TCGA-F1-6874         TCGA-F1-6875         TCGA-FP-7735 
"19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" 
        TCGA-FP-7829         TCGA-FP-7916         TCGA-FP-7998 
"19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" 
        TCGA-FP-8099         TCGA-FP-8209         TCGA-FP-8210 
"19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" 
        TCGA-FP-8631         TCGA-HJ-7597         TCGA-IN-7806 
      "19Q LOSS CNV" "19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" 
        TCGA-IN-7808         TCGA-IP-7968 
"19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" 
        TCGA-B7-5816         TCGA-B7-5818         TCGA-BR-6452 
"19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" 
        TCGA-BR-6455         TCGA-BR-6457         TCGA-BR-6458 
"19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" 
        TCGA-BR-6563         TCGA-BR-6564         TCGA-BR-6565 
"19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE"       "19Q LOSS CNV" 
        TCGA-BR-6566         TCGA-BR-6705         TCGA-BR-6706 
"19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" 
        TCGA-BR-6707         TCGA-BR-6709         TCGA-BR-6710 
"19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" 
        TCGA-BR-6801         TCGA-BR-6802         TCGA-BR-6803 
"19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" 
        TCGA-BR-6852         TCGA-BR-7196         TCGA-BR-7197 
"19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" 
        TCGA-BR-7703         TCGA-BR-7704         TCGA-BR-7707 
"19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" 
        TCGA-BR-7715         TCGA-BR-7716         TCGA-BR-7717 
"19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" 
        TCGA-BR-7722         TCGA-BR-7723         TCGA-BR-7851 
"19Q LOSS WILD-TYPE"       "19Q LOSS CNV" "19Q LOSS WILD-TYPE" 
        TCGA-BR-7901         TCGA-BR-7957         TCGA-BR-7958 
"19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" 
        TCGA-BR-7959         TCGA-BR-8059         TCGA-BR-8060 
"19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE"       "19Q LOSS CNV" 
        TCGA-BR-8077         TCGA-BR-8078         TCGA-BR-8080 
"19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" 
        TCGA-BR-8081         TCGA-BR-8284         TCGA-BR-8285 
"19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" 
        TCGA-BR-8286         TCGA-BR-8289         TCGA-BR-8291 
"19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" 
        TCGA-BR-8295         TCGA-BR-8296         TCGA-BR-8297 
"19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" 
        TCGA-BR-8592         TCGA-BR-A4IU         TCGA-BR-A4IV 
"19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" 
        TCGA-BR-A4IY         TCGA-BR-A4IZ         TCGA-BR-A4J1 
"19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" 
        TCGA-BR-A4J2         TCGA-BR-A4J4         TCGA-BR-A4J5 
"19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" 
        TCGA-BR-A4J6         TCGA-BR-A4J8         TCGA-BR-A4J9 
"19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" 
        TCGA-BR-A4PF         TCGA-BR-A4QI         TCGA-BR-A4QL 
"19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" 
        TCGA-CD-5798         TCGA-CD-5799         TCGA-CD-5800 
"19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" 
        TCGA-CD-5801         TCGA-CD-5802         TCGA-CD-5803 
"19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" 
        TCGA-CG-4300         TCGA-CG-4301         TCGA-CG-4304 
"19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" 
        TCGA-CG-4305         TCGA-CG-4306         TCGA-CG-4436 
"19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE"       "19Q LOSS CNV" 
        TCGA-CG-4437         TCGA-CG-4438         TCGA-CG-4440 
"19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE"       "19Q LOSS CNV" 
        TCGA-CG-4441         TCGA-CG-4443         TCGA-CG-4444 
"19Q LOSS WILD-TYPE"       "19Q LOSS CNV" "19Q LOSS WILD-TYPE" 
        TCGA-CG-4449         TCGA-CG-4455         TCGA-CG-4460 
"19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" 
        TCGA-CG-4462         TCGA-CG-4465         TCGA-CG-4466 
"19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE"       "19Q LOSS CNV" 
        TCGA-CG-4469         TCGA-CG-4472         TCGA-CG-4474 
"19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" 
        TCGA-CG-4477         TCGA-CG-5716         TCGA-CG-5717 
"19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" 
        TCGA-CG-5718         TCGA-CG-5719         TCGA-CG-5720 
"19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" 
        TCGA-CG-5721         TCGA-CG-5722         TCGA-CG-5723 
"19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" 
        TCGA-CG-5724         TCGA-CG-5725         TCGA-CG-5726 
"19Q LOSS WILD-TYPE"       "19Q LOSS CNV" "19Q LOSS WILD-TYPE" 
        TCGA-CG-5727         TCGA-CG-5728         TCGA-CG-5730 
"19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" 
        TCGA-CG-5732         TCGA-CG-5733         TCGA-CG-5734 
      "19Q LOSS CNV" "19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" 
        TCGA-D7-5577         TCGA-D7-5578         TCGA-D7-5579 
"19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" 
        TCGA-D7-6518         TCGA-D7-6519         TCGA-D7-6520 
"19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" 
        TCGA-D7-6521         TCGA-D7-6522         TCGA-D7-6524 
"19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" 
        TCGA-D7-6525         TCGA-D7-6526         TCGA-D7-6527 
"19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" 
        TCGA-D7-6528         TCGA-D7-6815         TCGA-D7-6817 
"19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" 
        TCGA-D7-6818         TCGA-D7-6820         TCGA-D7-6822 
"19Q LOSS WILD-TYPE"       "19Q LOSS CNV" "19Q LOSS WILD-TYPE" 
        TCGA-EQ-5647         TCGA-EQ-8122         TCGA-F1-6177 
      "19Q LOSS CNV" "19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" 
        TCGA-F1-6874         TCGA-F1-6875         TCGA-FP-7735 
"19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" 
        TCGA-FP-7829         TCGA-FP-7916         TCGA-FP-7998 
"19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" 
        TCGA-FP-8099         TCGA-FP-8209         TCGA-FP-8210 
"19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" 
        TCGA-FP-8631         TCGA-HJ-7597         TCGA-IN-7806 
      "19Q LOSS CNV" "19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" 
        TCGA-IN-7808         TCGA-IP-7968 
"19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" 
[1] "hr=" "1.1"
D70V2, continuous
D70V3, binary
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  19Q LOSS CNV          4   10
  19Q LOSS WILD-TYPE   68   98
        clus
vv       19Q LOSS CNV 19Q LOSS WILD-TYPE
  FEMALE            4                 68
  MALE             10                 98
                    vv
clus                 STOMACH  ADENOCARCINOMA  DIFFUSE TYPE
  19Q LOSS CNV                                           0
  19Q LOSS WILD-TYPE                                    10
                    vv
clus                 STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  19Q LOSS CNV                                                            1
  19Q LOSS WILD-TYPE                                                     15
                    vv
clus                 STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  19Q LOSS CNV                                                                       1
  19Q LOSS WILD-TYPE                                                                 7
                    vv
clus                 STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE
  19Q LOSS CNV                                                              0
  19Q LOSS WILD-TYPE                                                        3
                    vv
clus                 STOMACH ADENOCARCINOMA  SIGNET RING TYPE
  19Q LOSS CNV                                              0
  19Q LOSS WILD-TYPE                                        1
                    vv
clus                 STOMACH ADENOCARCINOMA - DIFFUSE TYPE
  19Q LOSS CNV                                           0
  19Q LOSS WILD-TYPE                                    16
                    vv
clus                 STOMACH ADENOCARCINOMA - NOT OTHERWISE SPECIFIED (NOS)
  19Q LOSS CNV                                                            6
  19Q LOSS WILD-TYPE                                                     67
                    vv
clus                 STOMACH INTESTINAL ADENOCARCINOMA - MUCINOUS TYPE
  19Q LOSS CNV                                                       0
  19Q LOSS WILD-TYPE                                                 7
                    vv
clus                 STOMACH INTESTINAL ADENOCARCINOMA - PAPILLARY TYPE
  19Q LOSS CNV                                                        0
  19Q LOSS WILD-TYPE                                                  3
                    vv
clus                 STOMACH INTESTINAL ADENOCARCINOMA - TUBULAR TYPE
  19Q LOSS CNV                                                      1
  19Q LOSS WILD-TYPE                                                9
                    vv
clus                 STOMACH INTESTINAL ADENOCARCINOMA - TYPE NOT OTHERWISE SPECIFIED (NOS)
  19Q LOSS CNV                                                                            5
  19Q LOSS WILD-TYPE                                                                     23
D70V4, multiclass
                    vv
clus                 T1 T2 T3 T4
  19Q LOSS CNV        1  5  4  1
  19Q LOSS WILD-TYPE  5 47 52 17
D70V5, multiclass
    clus
vv   19Q LOSS CNV 19Q LOSS WILD-TYPE
  T1            1                  5
  T2            5                 47
  T3            4                 52
  T4            1                 17
                    vv
clus                 N0 N1 N2 N3
  19Q LOSS CNV        5  2  1  3
  19Q LOSS WILD-TYPE 39 47 22 12
D70V6, multiclass
    clus
vv   19Q LOSS CNV 19Q LOSS WILD-TYPE
  N0            5                 39
  N1            2                 47
  N2            1                 22
  N3            3                 12
                    vv
clus                  M0  M1  MX
  19Q LOSS CNV        10   2   0
  19Q LOSS WILD-TYPE 108  14   8
D70V7, multiclass
    clus
vv   19Q LOSS CNV 19Q LOSS WILD-TYPE
  M0           10                108
  M1            2                 14
  MX            0                  8
                    vv
clus                  I II III IV
  19Q LOSS CNV        4  3   1  3
  19Q LOSS WILD-TYPE 20 34  38 23
D70V8, multiclass
     clus
vv    19Q LOSS CNV 19Q LOSS WILD-TYPE
  I              4                 20
  II             3                 34
  III            1                 38
  IV             3                 23
D70V9, binary
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  19Q LOSS CNV          0   14
  19Q LOSS WILD-TYPE    5  161
     clus
vv    19Q LOSS CNV 19Q LOSS WILD-TYPE
  NO             0                  5
  YES           14                161
                    vv
clus                  R0  R1  R2  RX
  19Q LOSS CNV        11   0   2   1
  19Q LOSS WILD-TYPE 114   7  10  24
D70V10, multiclass
    clus
vv   19Q LOSS CNV 19Q LOSS WILD-TYPE
  R0           11                114
  R1            0                  7
  R2            2                 10
  RX            1                 24
D70V11, continuous

Clustering(71) Variable = 20p loss
D71V1, survival
                    sevent
clus2                  0   1
  20P LOSS CNV         2   1
  20P LOSS WILD-TYPE 122  18
      20P LOSS CNV 20P LOSS WILD-TYPE 
                 3                140 
      20P LOSS CNV 20P LOSS WILD-TYPE 
                 1                 18 
$`20P LOSS CNV`
TCGA-CG-4301 TCGA-D7-6519 TCGA-EQ-5647 
        3.02        15.65         0.62 

$`20P LOSS WILD-TYPE`
TCGA-B7-5816 TCGA-B7-5818 TCGA-BR-6452 TCGA-BR-6455 TCGA-BR-6457 TCGA-BR-6458 
        5.62         0.10         0.95         1.41         1.35         1.35 
TCGA-BR-6563 TCGA-BR-6564 TCGA-BR-6565 TCGA-BR-6566 TCGA-BR-6705 TCGA-BR-6706 
        0.85         0.82         0.62         0.62         1.71         2.17 
TCGA-BR-6707 TCGA-BR-6709 TCGA-BR-6710 TCGA-BR-6801 TCGA-BR-6802 TCGA-BR-6803 
        0.99         1.22         0.66         1.12         0.76         0.66 
TCGA-BR-6852 TCGA-BR-7196 TCGA-BR-7197 TCGA-BR-7703 TCGA-BR-7704 TCGA-BR-7707 
        0.26         1.22         1.48         0.46         1.25         0.13 
TCGA-BR-7715 TCGA-BR-7716 TCGA-BR-7717 TCGA-BR-7722 TCGA-BR-7723 TCGA-BR-7851 
        1.05         0.82         0.69         0.16         4.54         0.99 
TCGA-BR-7901 TCGA-BR-7957 TCGA-BR-7958 TCGA-BR-7959 TCGA-BR-8059 TCGA-BR-8060 
        0.95         0.69         0.16         1.08         0.82         1.32 
TCGA-BR-8077 TCGA-BR-8078 TCGA-BR-8080 TCGA-BR-8081 TCGA-BR-8284 TCGA-BR-8285 
        0.69         0.95         0.49         0.46         0.72         0.26 
TCGA-BR-8286 TCGA-BR-8289 TCGA-BR-8291 TCGA-BR-8295 TCGA-BR-8296 TCGA-BR-8297 
        0.43         0.26         1.18         1.55         1.48         0.76 
TCGA-BR-8592 TCGA-BR-A4IU TCGA-BR-A4IV TCGA-BR-A4IY TCGA-BR-A4IZ TCGA-BR-A4J1 
        0.20         0.59         0.92         0.39         0.79         0.72 
TCGA-BR-A4J2 TCGA-BR-A4J4 TCGA-BR-A4J5 TCGA-BR-A4J6 TCGA-BR-A4J8 TCGA-BR-A4J9 
        0.79         0.53         0.43         0.13         0.23         0.10 
TCGA-BR-A4PF TCGA-BR-A4QI TCGA-BR-A4QL TCGA-CD-5798 TCGA-CD-5799 TCGA-CD-5800 
        0.72         0.49         2.24         0.82         0.69         0.36 
TCGA-CD-5801 TCGA-CD-5802 TCGA-CD-5803 TCGA-CG-4300 TCGA-CG-4304 TCGA-CG-4305 
        0.49         0.30         0.07        20.02        27.02        15.95 
TCGA-CG-4306 TCGA-CG-4436 TCGA-CG-4437 TCGA-CG-4438 TCGA-CG-4440 TCGA-CG-4441 
        1.02        52.96         8.05        54.05         4.01        14.01 
TCGA-CG-4443 TCGA-CG-4444 TCGA-CG-4449 TCGA-CG-4455 TCGA-CG-4460 TCGA-CG-4462 
       29.98        47.05        19.07        12.03        21.99         1.02 
TCGA-CG-4465 TCGA-CG-4466 TCGA-CG-4469 TCGA-CG-4472 TCGA-CG-4474 TCGA-CG-4477 
        8.98        18.94         7.07        12.00         1.02         1.02 
TCGA-CG-5716 TCGA-CG-5717 TCGA-CG-5718 TCGA-CG-5719 TCGA-CG-5720 TCGA-CG-5721 
        1.02         6.94         1.02         1.02         0.99         5.98 
TCGA-CG-5722 TCGA-CG-5723 TCGA-CG-5724 TCGA-CG-5725 TCGA-CG-5726 TCGA-CG-5727 
        0.95        70.06        12.03        15.02        28.96        31.04 
TCGA-CG-5728 TCGA-CG-5730 TCGA-CG-5732 TCGA-CG-5733 TCGA-CG-5734 TCGA-D7-5577 
       65.10         4.01        55.04        21.07         7.99         8.65 
TCGA-D7-5578 TCGA-D7-5579 TCGA-D7-6518 TCGA-D7-6520 TCGA-D7-6521 TCGA-D7-6522 
        3.58         4.54         9.80         9.63         8.19         6.90 
TCGA-D7-6524 TCGA-D7-6525 TCGA-D7-6526 TCGA-D7-6527 TCGA-D7-6528 TCGA-D7-6815 
        0.69         5.95         6.61         4.14         1.68         3.65 
TCGA-D7-6817 TCGA-D7-6818 TCGA-D7-6820 TCGA-D7-6822 TCGA-EQ-8122 TCGA-F1-6177 
        4.70         4.04         2.93         4.27         7.79         6.54 
TCGA-F1-6874 TCGA-F1-6875 TCGA-FP-7735 TCGA-FP-7829 TCGA-FP-7916 TCGA-FP-7998 
        2.01        72.23         0.39         0.20         3.02         3.58 
TCGA-FP-8099 TCGA-FP-8209 TCGA-FP-8210 TCGA-FP-8631 TCGA-HJ-7597 TCGA-IN-7806 
        1.02        59.05         5.03         0.56        26.43         6.87 
TCGA-IN-7808 TCGA-IP-7968 
        3.55         2.53 

      20P LOSS CNV 20P LOSS WILD-TYPE 
              0.62               0.07 
      20P LOSS CNV 20P LOSS WILD-TYPE 
             15.65              72.23 
      20P LOSS CNV 20P LOSS WILD-TYPE 
             3.020              1.235 
[1] "0.6 - 15.7 (3.0)" "0.1 - 72.2 (1.2)"
        TCGA-B7-5816         TCGA-B7-5818         TCGA-BR-6452 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-BR-6455         TCGA-BR-6457         TCGA-BR-6458 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-BR-6563         TCGA-BR-6564         TCGA-BR-6565 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-BR-6566         TCGA-BR-6705         TCGA-BR-6706 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-BR-6707         TCGA-BR-6709         TCGA-BR-6710 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-BR-6801         TCGA-BR-6802         TCGA-BR-6803 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-BR-6852         TCGA-BR-7196         TCGA-BR-7197 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-BR-7703         TCGA-BR-7704         TCGA-BR-7707 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-BR-7715         TCGA-BR-7716         TCGA-BR-7717 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-BR-7722         TCGA-BR-7723         TCGA-BR-7851 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-BR-7901         TCGA-BR-7957         TCGA-BR-7958 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-BR-7959         TCGA-BR-8059         TCGA-BR-8060 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-BR-8077         TCGA-BR-8078         TCGA-BR-8080 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-BR-8081         TCGA-BR-8284         TCGA-BR-8285 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-BR-8286         TCGA-BR-8289         TCGA-BR-8291 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-BR-8295         TCGA-BR-8296         TCGA-BR-8297 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-BR-8592         TCGA-BR-A4IU         TCGA-BR-A4IV 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-BR-A4IY         TCGA-BR-A4IZ         TCGA-BR-A4J1 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-BR-A4J2         TCGA-BR-A4J4         TCGA-BR-A4J5 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-BR-A4J6         TCGA-BR-A4J8         TCGA-BR-A4J9 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-BR-A4PF         TCGA-BR-A4QI         TCGA-BR-A4QL 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-CD-5798         TCGA-CD-5799         TCGA-CD-5800 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-CD-5801         TCGA-CD-5802         TCGA-CD-5803 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-CG-4300         TCGA-CG-4301         TCGA-CG-4304 
"20P LOSS WILD-TYPE"       "20P LOSS CNV" "20P LOSS WILD-TYPE" 
        TCGA-CG-4305         TCGA-CG-4306         TCGA-CG-4436 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-CG-4437         TCGA-CG-4438         TCGA-CG-4440 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-CG-4441         TCGA-CG-4443         TCGA-CG-4444 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-CG-4449         TCGA-CG-4455         TCGA-CG-4460 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-CG-4462         TCGA-CG-4465         TCGA-CG-4466 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-CG-4469         TCGA-CG-4472         TCGA-CG-4474 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-CG-4477         TCGA-CG-5716         TCGA-CG-5717 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-CG-5718         TCGA-CG-5719         TCGA-CG-5720 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-CG-5721         TCGA-CG-5722         TCGA-CG-5723 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-CG-5724         TCGA-CG-5725         TCGA-CG-5726 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-CG-5727         TCGA-CG-5728         TCGA-CG-5730 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-CG-5732         TCGA-CG-5733         TCGA-CG-5734 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-D7-5577         TCGA-D7-5578         TCGA-D7-5579 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-D7-6518         TCGA-D7-6519         TCGA-D7-6520 
"20P LOSS WILD-TYPE"       "20P LOSS CNV" "20P LOSS WILD-TYPE" 
        TCGA-D7-6521         TCGA-D7-6522         TCGA-D7-6524 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-D7-6525         TCGA-D7-6526         TCGA-D7-6527 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-D7-6528         TCGA-D7-6815         TCGA-D7-6817 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-D7-6818         TCGA-D7-6820         TCGA-D7-6822 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-EQ-5647         TCGA-EQ-8122         TCGA-F1-6177 
      "20P LOSS CNV" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-F1-6874         TCGA-F1-6875         TCGA-FP-7735 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-FP-7829         TCGA-FP-7916         TCGA-FP-7998 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-FP-8099         TCGA-FP-8209         TCGA-FP-8210 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-FP-8631         TCGA-HJ-7597         TCGA-IN-7806 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-IN-7808         TCGA-IP-7968 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-B7-5816         TCGA-B7-5818         TCGA-BR-6452 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-BR-6455         TCGA-BR-6457         TCGA-BR-6458 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-BR-6563         TCGA-BR-6564         TCGA-BR-6565 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-BR-6566         TCGA-BR-6705         TCGA-BR-6706 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-BR-6707         TCGA-BR-6709         TCGA-BR-6710 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-BR-6801         TCGA-BR-6802         TCGA-BR-6803 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-BR-6852         TCGA-BR-7196         TCGA-BR-7197 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-BR-7703         TCGA-BR-7704         TCGA-BR-7707 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-BR-7715         TCGA-BR-7716         TCGA-BR-7717 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-BR-7722         TCGA-BR-7723         TCGA-BR-7851 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-BR-7901         TCGA-BR-7957         TCGA-BR-7958 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-BR-7959         TCGA-BR-8059         TCGA-BR-8060 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-BR-8077         TCGA-BR-8078         TCGA-BR-8080 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-BR-8081         TCGA-BR-8284         TCGA-BR-8285 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-BR-8286         TCGA-BR-8289         TCGA-BR-8291 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-BR-8295         TCGA-BR-8296         TCGA-BR-8297 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-BR-8592         TCGA-BR-A4IU         TCGA-BR-A4IV 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-BR-A4IY         TCGA-BR-A4IZ         TCGA-BR-A4J1 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-BR-A4J2         TCGA-BR-A4J4         TCGA-BR-A4J5 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-BR-A4J6         TCGA-BR-A4J8         TCGA-BR-A4J9 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-BR-A4PF         TCGA-BR-A4QI         TCGA-BR-A4QL 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-CD-5798         TCGA-CD-5799         TCGA-CD-5800 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-CD-5801         TCGA-CD-5802         TCGA-CD-5803 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-CG-4300         TCGA-CG-4301         TCGA-CG-4304 
"20P LOSS WILD-TYPE"       "20P LOSS CNV" "20P LOSS WILD-TYPE" 
        TCGA-CG-4305         TCGA-CG-4306         TCGA-CG-4436 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-CG-4437         TCGA-CG-4438         TCGA-CG-4440 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-CG-4441         TCGA-CG-4443         TCGA-CG-4444 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-CG-4449         TCGA-CG-4455         TCGA-CG-4460 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-CG-4462         TCGA-CG-4465         TCGA-CG-4466 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-CG-4469         TCGA-CG-4472         TCGA-CG-4474 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-CG-4477         TCGA-CG-5716         TCGA-CG-5717 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-CG-5718         TCGA-CG-5719         TCGA-CG-5720 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-CG-5721         TCGA-CG-5722         TCGA-CG-5723 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-CG-5724         TCGA-CG-5725         TCGA-CG-5726 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-CG-5727         TCGA-CG-5728         TCGA-CG-5730 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-CG-5732         TCGA-CG-5733         TCGA-CG-5734 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-D7-5577         TCGA-D7-5578         TCGA-D7-5579 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-D7-6518         TCGA-D7-6519         TCGA-D7-6520 
"20P LOSS WILD-TYPE"       "20P LOSS CNV" "20P LOSS WILD-TYPE" 
        TCGA-D7-6521         TCGA-D7-6522         TCGA-D7-6524 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-D7-6525         TCGA-D7-6526         TCGA-D7-6527 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-D7-6528         TCGA-D7-6815         TCGA-D7-6817 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-D7-6818         TCGA-D7-6820         TCGA-D7-6822 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-EQ-5647         TCGA-EQ-8122         TCGA-F1-6177 
      "20P LOSS CNV" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-F1-6874         TCGA-F1-6875         TCGA-FP-7735 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-FP-7829         TCGA-FP-7916         TCGA-FP-7998 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-FP-8099         TCGA-FP-8209         TCGA-FP-8210 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-FP-8631         TCGA-HJ-7597         TCGA-IN-7806 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-IN-7808         TCGA-IP-7968 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-B7-5816         TCGA-B7-5818         TCGA-BR-6452 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-BR-6455         TCGA-BR-6457         TCGA-BR-6458 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-BR-6563         TCGA-BR-6564         TCGA-BR-6565 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-BR-6566         TCGA-BR-6705         TCGA-BR-6706 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-BR-6707         TCGA-BR-6709         TCGA-BR-6710 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-BR-6801         TCGA-BR-6802         TCGA-BR-6803 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-BR-6852         TCGA-BR-7196         TCGA-BR-7197 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-BR-7703         TCGA-BR-7704         TCGA-BR-7707 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-BR-7715         TCGA-BR-7716         TCGA-BR-7717 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-BR-7722         TCGA-BR-7723         TCGA-BR-7851 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-BR-7901         TCGA-BR-7957         TCGA-BR-7958 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-BR-7959         TCGA-BR-8059         TCGA-BR-8060 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-BR-8077         TCGA-BR-8078         TCGA-BR-8080 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-BR-8081         TCGA-BR-8284         TCGA-BR-8285 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-BR-8286         TCGA-BR-8289         TCGA-BR-8291 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-BR-8295         TCGA-BR-8296         TCGA-BR-8297 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-BR-8592         TCGA-BR-A4IU         TCGA-BR-A4IV 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-BR-A4IY         TCGA-BR-A4IZ         TCGA-BR-A4J1 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-BR-A4J2         TCGA-BR-A4J4         TCGA-BR-A4J5 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-BR-A4J6         TCGA-BR-A4J8         TCGA-BR-A4J9 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-BR-A4PF         TCGA-BR-A4QI         TCGA-BR-A4QL 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-CD-5798         TCGA-CD-5799         TCGA-CD-5800 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-CD-5801         TCGA-CD-5802         TCGA-CD-5803 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-CG-4300         TCGA-CG-4301         TCGA-CG-4304 
"20P LOSS WILD-TYPE"       "20P LOSS CNV" "20P LOSS WILD-TYPE" 
        TCGA-CG-4305         TCGA-CG-4306         TCGA-CG-4436 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-CG-4437         TCGA-CG-4438         TCGA-CG-4440 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-CG-4441         TCGA-CG-4443         TCGA-CG-4444 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-CG-4449         TCGA-CG-4455         TCGA-CG-4460 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-CG-4462         TCGA-CG-4465         TCGA-CG-4466 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-CG-4469         TCGA-CG-4472         TCGA-CG-4474 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-CG-4477         TCGA-CG-5716         TCGA-CG-5717 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-CG-5718         TCGA-CG-5719         TCGA-CG-5720 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-CG-5721         TCGA-CG-5722         TCGA-CG-5723 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-CG-5724         TCGA-CG-5725         TCGA-CG-5726 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-CG-5727         TCGA-CG-5728         TCGA-CG-5730 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-CG-5732         TCGA-CG-5733         TCGA-CG-5734 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-D7-5577         TCGA-D7-5578         TCGA-D7-5579 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-D7-6518         TCGA-D7-6519         TCGA-D7-6520 
"20P LOSS WILD-TYPE"       "20P LOSS CNV" "20P LOSS WILD-TYPE" 
        TCGA-D7-6521         TCGA-D7-6522         TCGA-D7-6524 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-D7-6525         TCGA-D7-6526         TCGA-D7-6527 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-D7-6528         TCGA-D7-6815         TCGA-D7-6817 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-D7-6818         TCGA-D7-6820         TCGA-D7-6822 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-EQ-5647         TCGA-EQ-8122         TCGA-F1-6177 
      "20P LOSS CNV" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-F1-6874         TCGA-F1-6875         TCGA-FP-7735 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-FP-7829         TCGA-FP-7916         TCGA-FP-7998 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-FP-8099         TCGA-FP-8209         TCGA-FP-8210 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-FP-8631         TCGA-HJ-7597         TCGA-IN-7806 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-IN-7808         TCGA-IP-7968 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
[1] "hr=" "2.7"
D71V2, continuous
D71V3, binary
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  20P LOSS CNV          4    1
  20P LOSS WILD-TYPE   68  107
        clus
vv       20P LOSS CNV 20P LOSS WILD-TYPE
  FEMALE            4                 68
  MALE              1                107
                    vv
clus                 STOMACH  ADENOCARCINOMA  DIFFUSE TYPE
  20P LOSS CNV                                           0
  20P LOSS WILD-TYPE                                    10
                    vv
clus                 STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  20P LOSS CNV                                                            0
  20P LOSS WILD-TYPE                                                     16
                    vv
clus                 STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  20P LOSS CNV                                                                       0
  20P LOSS WILD-TYPE                                                                 8
                    vv
clus                 STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE
  20P LOSS CNV                                                              0
  20P LOSS WILD-TYPE                                                        3
                    vv
clus                 STOMACH ADENOCARCINOMA  SIGNET RING TYPE
  20P LOSS CNV                                              0
  20P LOSS WILD-TYPE                                        1
                    vv
clus                 STOMACH ADENOCARCINOMA - DIFFUSE TYPE
  20P LOSS CNV                                           1
  20P LOSS WILD-TYPE                                    15
                    vv
clus                 STOMACH ADENOCARCINOMA - NOT OTHERWISE SPECIFIED (NOS)
  20P LOSS CNV                                                            3
  20P LOSS WILD-TYPE                                                     70
                    vv
clus                 STOMACH INTESTINAL ADENOCARCINOMA - MUCINOUS TYPE
  20P LOSS CNV                                                       1
  20P LOSS WILD-TYPE                                                 6
                    vv
clus                 STOMACH INTESTINAL ADENOCARCINOMA - PAPILLARY TYPE
  20P LOSS CNV                                                        0
  20P LOSS WILD-TYPE                                                  3
                    vv
clus                 STOMACH INTESTINAL ADENOCARCINOMA - TUBULAR TYPE
  20P LOSS CNV                                                      0
  20P LOSS WILD-TYPE                                               10
                    vv
clus                 STOMACH INTESTINAL ADENOCARCINOMA - TYPE NOT OTHERWISE SPECIFIED (NOS)
  20P LOSS CNV                                                                            0
  20P LOSS WILD-TYPE                                                                     28
D71V4, multiclass
                    vv
clus                 T1 T2 T3 T4
  20P LOSS CNV        0  3  0  2
  20P LOSS WILD-TYPE  6 49 56 16
D71V5, multiclass
    clus
vv   20P LOSS CNV 20P LOSS WILD-TYPE
  T1            0                  6
  T2            3                 49
  T3            0                 56
  T4            2                 16
                    vv
clus                 N0 N1 N2 N3
  20P LOSS CNV        1  2  0  2
  20P LOSS WILD-TYPE 43 47 23 13
D71V6, multiclass
    clus
vv   20P LOSS CNV 20P LOSS WILD-TYPE
  N0            1                 43
  N1            2                 47
  N2            0                 23
  N3            2                 13
                    vv
clus                  M0  M1  MX
  20P LOSS CNV         3   2   0
  20P LOSS WILD-TYPE 115  14   8
D71V7, multiclass
    clus
vv   20P LOSS CNV 20P LOSS WILD-TYPE
  M0            3                115
  M1            2                 14
  MX            0                  8
                    vv
clus                  I II III IV
  20P LOSS CNV        1  0   1  3
  20P LOSS WILD-TYPE 23 37  38 23
D71V8, multiclass
     clus
vv    20P LOSS CNV 20P LOSS WILD-TYPE
  I              1                 23
  II             0                 37
  III            1                 38
  IV             3                 23
D71V9, binary
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  20P LOSS CNV          1    4
  20P LOSS WILD-TYPE    4  171
     clus
vv    20P LOSS CNV 20P LOSS WILD-TYPE
  NO             1                  4
  YES            4                171
                    vv
clus                  R0  R1  R2  RX
  20P LOSS CNV         1   1   2   1
  20P LOSS WILD-TYPE 124   6  10  24
D71V10, multiclass
    clus
vv   20P LOSS CNV 20P LOSS WILD-TYPE
  R0            1                124
  R1            1                  6
  R2            2                 10
  RX            1                 24
D71V11, continuous

Clustering(72) Variable = 21q loss
D72V1, survival
                    sevent
clus2                  0   1
  21Q LOSS CNV        22   4
  21Q LOSS WILD-TYPE 102  15
      21Q LOSS CNV 21Q LOSS WILD-TYPE 
                26                117 
      21Q LOSS CNV 21Q LOSS WILD-TYPE 
                 4                 15 
$`21Q LOSS CNV`
TCGA-B7-5818 TCGA-BR-6458 TCGA-BR-7704 TCGA-BR-7715 TCGA-BR-7959 TCGA-BR-8284 
        0.10         1.35         1.25         1.05         1.08         0.72 
TCGA-BR-8297 TCGA-BR-A4J1 TCGA-BR-A4J8 TCGA-BR-A4PF TCGA-CG-4438 TCGA-CG-4466 
        0.76         0.72         0.23         0.72        54.05        18.94 
TCGA-CG-4477 TCGA-CG-5719 TCGA-CG-5724 TCGA-CG-5725 TCGA-CG-5728 TCGA-CG-5730 
        1.02         1.02        12.03        15.02        65.10         4.01 
TCGA-D7-5579 TCGA-D7-6525 TCGA-D7-6526 TCGA-D7-6817 TCGA-EQ-5647 TCGA-FP-7829 
        4.54         5.95         6.61         4.70         0.62         0.20 
TCGA-FP-8099 TCGA-IN-7806 
        1.02         6.87 

$`21Q LOSS WILD-TYPE`
TCGA-B7-5816 TCGA-BR-6452 TCGA-BR-6455 TCGA-BR-6457 TCGA-BR-6563 TCGA-BR-6564 
        5.62         0.95         1.41         1.35         0.85         0.82 
TCGA-BR-6565 TCGA-BR-6566 TCGA-BR-6705 TCGA-BR-6706 TCGA-BR-6707 TCGA-BR-6709 
        0.62         0.62         1.71         2.17         0.99         1.22 
TCGA-BR-6710 TCGA-BR-6801 TCGA-BR-6802 TCGA-BR-6803 TCGA-BR-6852 TCGA-BR-7196 
        0.66         1.12         0.76         0.66         0.26         1.22 
TCGA-BR-7197 TCGA-BR-7703 TCGA-BR-7707 TCGA-BR-7716 TCGA-BR-7717 TCGA-BR-7722 
        1.48         0.46         0.13         0.82         0.69         0.16 
TCGA-BR-7723 TCGA-BR-7851 TCGA-BR-7901 TCGA-BR-7957 TCGA-BR-7958 TCGA-BR-8059 
        4.54         0.99         0.95         0.69         0.16         0.82 
TCGA-BR-8060 TCGA-BR-8077 TCGA-BR-8078 TCGA-BR-8080 TCGA-BR-8081 TCGA-BR-8285 
        1.32         0.69         0.95         0.49         0.46         0.26 
TCGA-BR-8286 TCGA-BR-8289 TCGA-BR-8291 TCGA-BR-8295 TCGA-BR-8296 TCGA-BR-8592 
        0.43         0.26         1.18         1.55         1.48         0.20 
TCGA-BR-A4IU TCGA-BR-A4IV TCGA-BR-A4IY TCGA-BR-A4IZ TCGA-BR-A4J2 TCGA-BR-A4J4 
        0.59         0.92         0.39         0.79         0.79         0.53 
TCGA-BR-A4J5 TCGA-BR-A4J6 TCGA-BR-A4J9 TCGA-BR-A4QI TCGA-BR-A4QL TCGA-CD-5798 
        0.43         0.13         0.10         0.49         2.24         0.82 
TCGA-CD-5799 TCGA-CD-5800 TCGA-CD-5801 TCGA-CD-5802 TCGA-CD-5803 TCGA-CG-4300 
        0.69         0.36         0.49         0.30         0.07        20.02 
TCGA-CG-4301 TCGA-CG-4304 TCGA-CG-4305 TCGA-CG-4306 TCGA-CG-4436 TCGA-CG-4437 
        3.02        27.02        15.95         1.02        52.96         8.05 
TCGA-CG-4440 TCGA-CG-4441 TCGA-CG-4443 TCGA-CG-4444 TCGA-CG-4449 TCGA-CG-4455 
        4.01        14.01        29.98        47.05        19.07        12.03 
TCGA-CG-4460 TCGA-CG-4462 TCGA-CG-4465 TCGA-CG-4469 TCGA-CG-4472 TCGA-CG-4474 
       21.99         1.02         8.98         7.07        12.00         1.02 
TCGA-CG-5716 TCGA-CG-5717 TCGA-CG-5718 TCGA-CG-5720 TCGA-CG-5721 TCGA-CG-5722 
        1.02         6.94         1.02         0.99         5.98         0.95 
TCGA-CG-5723 TCGA-CG-5726 TCGA-CG-5727 TCGA-CG-5732 TCGA-CG-5733 TCGA-CG-5734 
       70.06        28.96        31.04        55.04        21.07         7.99 
TCGA-D7-5577 TCGA-D7-5578 TCGA-D7-6518 TCGA-D7-6519 TCGA-D7-6520 TCGA-D7-6521 
        8.65         3.58         9.80        15.65         9.63         8.19 
TCGA-D7-6522 TCGA-D7-6524 TCGA-D7-6527 TCGA-D7-6528 TCGA-D7-6815 TCGA-D7-6818 
        6.90         0.69         4.14         1.68         3.65         4.04 
TCGA-D7-6820 TCGA-D7-6822 TCGA-EQ-8122 TCGA-F1-6177 TCGA-F1-6874 TCGA-F1-6875 
        2.93         4.27         7.79         6.54         2.01        72.23 
TCGA-FP-7735 TCGA-FP-7916 TCGA-FP-7998 TCGA-FP-8209 TCGA-FP-8210 TCGA-FP-8631 
        0.39         3.02         3.58        59.05         5.03         0.56 
TCGA-HJ-7597 TCGA-IN-7808 TCGA-IP-7968 
       26.43         3.55         2.53 

      21Q LOSS CNV 21Q LOSS WILD-TYPE 
              0.10               0.07 
      21Q LOSS CNV 21Q LOSS WILD-TYPE 
             65.10              72.23 
      21Q LOSS CNV 21Q LOSS WILD-TYPE 
             1.165              1.320 
[1] "0.1 - 65.1 (1.2)" "0.1 - 72.2 (1.3)"
        TCGA-B7-5816         TCGA-B7-5818         TCGA-BR-6452 
"21Q LOSS WILD-TYPE"       "21Q LOSS CNV" "21Q LOSS WILD-TYPE" 
        TCGA-BR-6455         TCGA-BR-6457         TCGA-BR-6458 
"21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE"       "21Q LOSS CNV" 
        TCGA-BR-6563         TCGA-BR-6564         TCGA-BR-6565 
"21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" 
        TCGA-BR-6566         TCGA-BR-6705         TCGA-BR-6706 
"21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" 
        TCGA-BR-6707         TCGA-BR-6709         TCGA-BR-6710 
"21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" 
        TCGA-BR-6801         TCGA-BR-6802         TCGA-BR-6803 
"21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" 
        TCGA-BR-6852         TCGA-BR-7196         TCGA-BR-7197 
"21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" 
        TCGA-BR-7703         TCGA-BR-7704         TCGA-BR-7707 
"21Q LOSS WILD-TYPE"       "21Q LOSS CNV" "21Q LOSS WILD-TYPE" 
        TCGA-BR-7715         TCGA-BR-7716         TCGA-BR-7717 
      "21Q LOSS CNV" "21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" 
        TCGA-BR-7722         TCGA-BR-7723         TCGA-BR-7851 
"21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" 
        TCGA-BR-7901         TCGA-BR-7957         TCGA-BR-7958 
"21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" 
        TCGA-BR-7959         TCGA-BR-8059         TCGA-BR-8060 
      "21Q LOSS CNV" "21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" 
        TCGA-BR-8077         TCGA-BR-8078         TCGA-BR-8080 
"21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" 
        TCGA-BR-8081         TCGA-BR-8284         TCGA-BR-8285 
"21Q LOSS WILD-TYPE"       "21Q LOSS CNV" "21Q LOSS WILD-TYPE" 
        TCGA-BR-8286         TCGA-BR-8289         TCGA-BR-8291 
"21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" 
        TCGA-BR-8295         TCGA-BR-8296         TCGA-BR-8297 
"21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE"       "21Q LOSS CNV" 
        TCGA-BR-8592         TCGA-BR-A4IU         TCGA-BR-A4IV 
"21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" 
        TCGA-BR-A4IY         TCGA-BR-A4IZ         TCGA-BR-A4J1 
"21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE"       "21Q LOSS CNV" 
        TCGA-BR-A4J2         TCGA-BR-A4J4         TCGA-BR-A4J5 
"21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" 
        TCGA-BR-A4J6         TCGA-BR-A4J8         TCGA-BR-A4J9 
"21Q LOSS WILD-TYPE"       "21Q LOSS CNV" "21Q LOSS WILD-TYPE" 
        TCGA-BR-A4PF         TCGA-BR-A4QI         TCGA-BR-A4QL 
      "21Q LOSS CNV" "21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" 
        TCGA-CD-5798         TCGA-CD-5799         TCGA-CD-5800 
"21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" 
        TCGA-CD-5801         TCGA-CD-5802         TCGA-CD-5803 
"21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" 
        TCGA-CG-4300         TCGA-CG-4301         TCGA-CG-4304 
"21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" 
        TCGA-CG-4305         TCGA-CG-4306         TCGA-CG-4436 
"21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" 
        TCGA-CG-4437         TCGA-CG-4438         TCGA-CG-4440 
"21Q LOSS WILD-TYPE"       "21Q LOSS CNV" "21Q LOSS WILD-TYPE" 
        TCGA-CG-4441         TCGA-CG-4443         TCGA-CG-4444 
"21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" 
        TCGA-CG-4449         TCGA-CG-4455         TCGA-CG-4460 
"21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" 
        TCGA-CG-4462         TCGA-CG-4465         TCGA-CG-4466 
"21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE"       "21Q LOSS CNV" 
        TCGA-CG-4469         TCGA-CG-4472         TCGA-CG-4474 
"21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" 
        TCGA-CG-4477         TCGA-CG-5716         TCGA-CG-5717 
      "21Q LOSS CNV" "21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" 
        TCGA-CG-5718         TCGA-CG-5719         TCGA-CG-5720 
"21Q LOSS WILD-TYPE"       "21Q LOSS CNV" "21Q LOSS WILD-TYPE" 
        TCGA-CG-5721         TCGA-CG-5722         TCGA-CG-5723 
"21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" 
        TCGA-CG-5724         TCGA-CG-5725         TCGA-CG-5726 
      "21Q LOSS CNV"       "21Q LOSS CNV" "21Q LOSS WILD-TYPE" 
        TCGA-CG-5727         TCGA-CG-5728         TCGA-CG-5730 
"21Q LOSS WILD-TYPE"       "21Q LOSS CNV"       "21Q LOSS CNV" 
        TCGA-CG-5732         TCGA-CG-5733         TCGA-CG-5734 
"21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" 
        TCGA-D7-5577         TCGA-D7-5578         TCGA-D7-5579 
"21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE"       "21Q LOSS CNV" 
        TCGA-D7-6518         TCGA-D7-6519         TCGA-D7-6520 
"21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" 
        TCGA-D7-6521         TCGA-D7-6522         TCGA-D7-6524 
"21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" 
        TCGA-D7-6525         TCGA-D7-6526         TCGA-D7-6527 
      "21Q LOSS CNV"       "21Q LOSS CNV" "21Q LOSS WILD-TYPE" 
        TCGA-D7-6528         TCGA-D7-6815         TCGA-D7-6817 
"21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE"       "21Q LOSS CNV" 
        TCGA-D7-6818         TCGA-D7-6820         TCGA-D7-6822 
"21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" 
        TCGA-EQ-5647         TCGA-EQ-8122         TCGA-F1-6177 
      "21Q LOSS CNV" "21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" 
        TCGA-F1-6874         TCGA-F1-6875         TCGA-FP-7735 
"21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" 
        TCGA-FP-7829         TCGA-FP-7916         TCGA-FP-7998 
      "21Q LOSS CNV" "21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" 
        TCGA-FP-8099         TCGA-FP-8209         TCGA-FP-8210 
      "21Q LOSS CNV" "21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" 
        TCGA-FP-8631         TCGA-HJ-7597         TCGA-IN-7806 
"21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE"       "21Q LOSS CNV" 
        TCGA-IN-7808         TCGA-IP-7968 
"21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" 
        TCGA-B7-5816         TCGA-B7-5818         TCGA-BR-6452 
"21Q LOSS WILD-TYPE"       "21Q LOSS CNV" "21Q LOSS WILD-TYPE" 
        TCGA-BR-6455         TCGA-BR-6457         TCGA-BR-6458 
"21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE"       "21Q LOSS CNV" 
        TCGA-BR-6563         TCGA-BR-6564         TCGA-BR-6565 
"21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" 
        TCGA-BR-6566         TCGA-BR-6705         TCGA-BR-6706 
"21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" 
        TCGA-BR-6707         TCGA-BR-6709         TCGA-BR-6710 
"21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" 
        TCGA-BR-6801         TCGA-BR-6802         TCGA-BR-6803 
"21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" 
        TCGA-BR-6852         TCGA-BR-7196         TCGA-BR-7197 
"21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" 
        TCGA-BR-7703         TCGA-BR-7704         TCGA-BR-7707 
"21Q LOSS WILD-TYPE"       "21Q LOSS CNV" "21Q LOSS WILD-TYPE" 
        TCGA-BR-7715         TCGA-BR-7716         TCGA-BR-7717 
      "21Q LOSS CNV" "21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" 
        TCGA-BR-7722         TCGA-BR-7723         TCGA-BR-7851 
"21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" 
        TCGA-BR-7901         TCGA-BR-7957         TCGA-BR-7958 
"21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" 
        TCGA-BR-7959         TCGA-BR-8059         TCGA-BR-8060 
      "21Q LOSS CNV" "21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" 
        TCGA-BR-8077         TCGA-BR-8078         TCGA-BR-8080 
"21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" 
        TCGA-BR-8081         TCGA-BR-8284         TCGA-BR-8285 
"21Q LOSS WILD-TYPE"       "21Q LOSS CNV" "21Q LOSS WILD-TYPE" 
        TCGA-BR-8286         TCGA-BR-8289         TCGA-BR-8291 
"21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" 
        TCGA-BR-8295         TCGA-BR-8296         TCGA-BR-8297 
"21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE"       "21Q LOSS CNV" 
        TCGA-BR-8592         TCGA-BR-A4IU         TCGA-BR-A4IV 
"21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" 
        TCGA-BR-A4IY         TCGA-BR-A4IZ         TCGA-BR-A4J1 
"21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE"       "21Q LOSS CNV" 
        TCGA-BR-A4J2         TCGA-BR-A4J4         TCGA-BR-A4J5 
"21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" 
        TCGA-BR-A4J6         TCGA-BR-A4J8         TCGA-BR-A4J9 
"21Q LOSS WILD-TYPE"       "21Q LOSS CNV" "21Q LOSS WILD-TYPE" 
        TCGA-BR-A4PF         TCGA-BR-A4QI         TCGA-BR-A4QL 
      "21Q LOSS CNV" "21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" 
        TCGA-CD-5798         TCGA-CD-5799         TCGA-CD-5800 
"21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" 
        TCGA-CD-5801         TCGA-CD-5802         TCGA-CD-5803 
"21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" 
        TCGA-CG-4300         TCGA-CG-4301         TCGA-CG-4304 
"21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" 
        TCGA-CG-4305         TCGA-CG-4306         TCGA-CG-4436 
"21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" 
        TCGA-CG-4437         TCGA-CG-4438         TCGA-CG-4440 
"21Q LOSS WILD-TYPE"       "21Q LOSS CNV" "21Q LOSS WILD-TYPE" 
        TCGA-CG-4441         TCGA-CG-4443         TCGA-CG-4444 
"21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" 
        TCGA-CG-4449         TCGA-CG-4455         TCGA-CG-4460 
"21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" 
        TCGA-CG-4462         TCGA-CG-4465         TCGA-CG-4466 
"21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE"       "21Q LOSS CNV" 
        TCGA-CG-4469         TCGA-CG-4472         TCGA-CG-4474 
"21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" 
        TCGA-CG-4477         TCGA-CG-5716         TCGA-CG-5717 
      "21Q LOSS CNV" "21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" 
        TCGA-CG-5718         TCGA-CG-5719         TCGA-CG-5720 
"21Q LOSS WILD-TYPE"       "21Q LOSS CNV" "21Q LOSS WILD-TYPE" 
        TCGA-CG-5721         TCGA-CG-5722         TCGA-CG-5723 
"21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" 
        TCGA-CG-5724         TCGA-CG-5725         TCGA-CG-5726 
      "21Q LOSS CNV"       "21Q LOSS CNV" "21Q LOSS WILD-TYPE" 
        TCGA-CG-5727         TCGA-CG-5728         TCGA-CG-5730 
"21Q LOSS WILD-TYPE"       "21Q LOSS CNV"       "21Q LOSS CNV" 
        TCGA-CG-5732         TCGA-CG-5733         TCGA-CG-5734 
"21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" 
        TCGA-D7-5577         TCGA-D7-5578         TCGA-D7-5579 
"21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE"       "21Q LOSS CNV" 
        TCGA-D7-6518         TCGA-D7-6519         TCGA-D7-6520 
"21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" 
        TCGA-D7-6521         TCGA-D7-6522         TCGA-D7-6524 
"21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" 
        TCGA-D7-6525         TCGA-D7-6526         TCGA-D7-6527 
      "21Q LOSS CNV"       "21Q LOSS CNV" "21Q LOSS WILD-TYPE" 
        TCGA-D7-6528         TCGA-D7-6815         TCGA-D7-6817 
"21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE"       "21Q LOSS CNV" 
        TCGA-D7-6818         TCGA-D7-6820         TCGA-D7-6822 
"21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" 
        TCGA-EQ-5647         TCGA-EQ-8122         TCGA-F1-6177 
      "21Q LOSS CNV" "21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" 
        TCGA-F1-6874         TCGA-F1-6875         TCGA-FP-7735 
"21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" 
        TCGA-FP-7829         TCGA-FP-7916         TCGA-FP-7998 
      "21Q LOSS CNV" "21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" 
        TCGA-FP-8099         TCGA-FP-8209         TCGA-FP-8210 
      "21Q LOSS CNV" "21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" 
        TCGA-FP-8631         TCGA-HJ-7597         TCGA-IN-7806 
"21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE"       "21Q LOSS CNV" 
        TCGA-IN-7808         TCGA-IP-7968 
"21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" 
        TCGA-B7-5816         TCGA-B7-5818         TCGA-BR-6452 
"21Q LOSS WILD-TYPE"       "21Q LOSS CNV" "21Q LOSS WILD-TYPE" 
        TCGA-BR-6455         TCGA-BR-6457         TCGA-BR-6458 
"21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE"       "21Q LOSS CNV" 
        TCGA-BR-6563         TCGA-BR-6564         TCGA-BR-6565 
"21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" 
        TCGA-BR-6566         TCGA-BR-6705         TCGA-BR-6706 
"21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" 
        TCGA-BR-6707         TCGA-BR-6709         TCGA-BR-6710 
"21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" 
        TCGA-BR-6801         TCGA-BR-6802         TCGA-BR-6803 
"21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" 
        TCGA-BR-6852         TCGA-BR-7196         TCGA-BR-7197 
"21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" 
        TCGA-BR-7703         TCGA-BR-7704         TCGA-BR-7707 
"21Q LOSS WILD-TYPE"       "21Q LOSS CNV" "21Q LOSS WILD-TYPE" 
        TCGA-BR-7715         TCGA-BR-7716         TCGA-BR-7717 
      "21Q LOSS CNV" "21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" 
        TCGA-BR-7722         TCGA-BR-7723         TCGA-BR-7851 
"21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" 
        TCGA-BR-7901         TCGA-BR-7957         TCGA-BR-7958 
"21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" 
        TCGA-BR-7959         TCGA-BR-8059         TCGA-BR-8060 
      "21Q LOSS CNV" "21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" 
        TCGA-BR-8077         TCGA-BR-8078         TCGA-BR-8080 
"21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" 
        TCGA-BR-8081         TCGA-BR-8284         TCGA-BR-8285 
"21Q LOSS WILD-TYPE"       "21Q LOSS CNV" "21Q LOSS WILD-TYPE" 
        TCGA-BR-8286         TCGA-BR-8289         TCGA-BR-8291 
"21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" 
        TCGA-BR-8295         TCGA-BR-8296         TCGA-BR-8297 
"21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE"       "21Q LOSS CNV" 
        TCGA-BR-8592         TCGA-BR-A4IU         TCGA-BR-A4IV 
"21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" 
        TCGA-BR-A4IY         TCGA-BR-A4IZ         TCGA-BR-A4J1 
"21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE"       "21Q LOSS CNV" 
        TCGA-BR-A4J2         TCGA-BR-A4J4         TCGA-BR-A4J5 
"21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" 
        TCGA-BR-A4J6         TCGA-BR-A4J8         TCGA-BR-A4J9 
"21Q LOSS WILD-TYPE"       "21Q LOSS CNV" "21Q LOSS WILD-TYPE" 
        TCGA-BR-A4PF         TCGA-BR-A4QI         TCGA-BR-A4QL 
      "21Q LOSS CNV" "21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" 
        TCGA-CD-5798         TCGA-CD-5799         TCGA-CD-5800 
"21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" 
        TCGA-CD-5801         TCGA-CD-5802         TCGA-CD-5803 
"21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" 
        TCGA-CG-4300         TCGA-CG-4301         TCGA-CG-4304 
"21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" 
        TCGA-CG-4305         TCGA-CG-4306         TCGA-CG-4436 
"21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" 
        TCGA-CG-4437         TCGA-CG-4438         TCGA-CG-4440 
"21Q LOSS WILD-TYPE"       "21Q LOSS CNV" "21Q LOSS WILD-TYPE" 
        TCGA-CG-4441         TCGA-CG-4443         TCGA-CG-4444 
"21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" 
        TCGA-CG-4449         TCGA-CG-4455         TCGA-CG-4460 
"21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" 
        TCGA-CG-4462         TCGA-CG-4465         TCGA-CG-4466 
"21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE"       "21Q LOSS CNV" 
        TCGA-CG-4469         TCGA-CG-4472         TCGA-CG-4474 
"21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" 
        TCGA-CG-4477         TCGA-CG-5716         TCGA-CG-5717 
      "21Q LOSS CNV" "21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" 
        TCGA-CG-5718         TCGA-CG-5719         TCGA-CG-5720 
"21Q LOSS WILD-TYPE"       "21Q LOSS CNV" "21Q LOSS WILD-TYPE" 
        TCGA-CG-5721         TCGA-CG-5722         TCGA-CG-5723 
"21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" 
        TCGA-CG-5724         TCGA-CG-5725         TCGA-CG-5726 
      "21Q LOSS CNV"       "21Q LOSS CNV" "21Q LOSS WILD-TYPE" 
        TCGA-CG-5727         TCGA-CG-5728         TCGA-CG-5730 
"21Q LOSS WILD-TYPE"       "21Q LOSS CNV"       "21Q LOSS CNV" 
        TCGA-CG-5732         TCGA-CG-5733         TCGA-CG-5734 
"21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" 
        TCGA-D7-5577         TCGA-D7-5578         TCGA-D7-5579 
"21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE"       "21Q LOSS CNV" 
        TCGA-D7-6518         TCGA-D7-6519         TCGA-D7-6520 
"21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" 
        TCGA-D7-6521         TCGA-D7-6522         TCGA-D7-6524 
"21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" 
        TCGA-D7-6525         TCGA-D7-6526         TCGA-D7-6527 
      "21Q LOSS CNV"       "21Q LOSS CNV" "21Q LOSS WILD-TYPE" 
        TCGA-D7-6528         TCGA-D7-6815         TCGA-D7-6817 
"21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE"       "21Q LOSS CNV" 
        TCGA-D7-6818         TCGA-D7-6820         TCGA-D7-6822 
"21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" 
        TCGA-EQ-5647         TCGA-EQ-8122         TCGA-F1-6177 
      "21Q LOSS CNV" "21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" 
        TCGA-F1-6874         TCGA-F1-6875         TCGA-FP-7735 
"21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" 
        TCGA-FP-7829         TCGA-FP-7916         TCGA-FP-7998 
      "21Q LOSS CNV" "21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" 
        TCGA-FP-8099         TCGA-FP-8209         TCGA-FP-8210 
      "21Q LOSS CNV" "21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" 
        TCGA-FP-8631         TCGA-HJ-7597         TCGA-IN-7806 
"21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE"       "21Q LOSS CNV" 
        TCGA-IN-7808         TCGA-IP-7968 
"21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" 
[1] "hr=" "1.3"
D72V2, continuous
D72V3, binary
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  21Q LOSS CNV         13   22
  21Q LOSS WILD-TYPE   59   86
        clus
vv       21Q LOSS CNV 21Q LOSS WILD-TYPE
  FEMALE           13                 59
  MALE             22                 86
                    vv
clus                 STOMACH  ADENOCARCINOMA  DIFFUSE TYPE
  21Q LOSS CNV                                           1
  21Q LOSS WILD-TYPE                                     9
                    vv
clus                 STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  21Q LOSS CNV                                                            4
  21Q LOSS WILD-TYPE                                                     12
                    vv
clus                 STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  21Q LOSS CNV                                                                       1
  21Q LOSS WILD-TYPE                                                                 7
                    vv
clus                 STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE
  21Q LOSS CNV                                                              1
  21Q LOSS WILD-TYPE                                                        2
                    vv
clus                 STOMACH ADENOCARCINOMA  SIGNET RING TYPE
  21Q LOSS CNV                                              0
  21Q LOSS WILD-TYPE                                        1
                    vv
clus                 STOMACH ADENOCARCINOMA - DIFFUSE TYPE
  21Q LOSS CNV                                           4
  21Q LOSS WILD-TYPE                                    12
                    vv
clus                 STOMACH ADENOCARCINOMA - NOT OTHERWISE SPECIFIED (NOS)
  21Q LOSS CNV                                                           11
  21Q LOSS WILD-TYPE                                                     62
                    vv
clus                 STOMACH INTESTINAL ADENOCARCINOMA - MUCINOUS TYPE
  21Q LOSS CNV                                                       3
  21Q LOSS WILD-TYPE                                                 4
                    vv
clus                 STOMACH INTESTINAL ADENOCARCINOMA - PAPILLARY TYPE
  21Q LOSS CNV                                                        0
  21Q LOSS WILD-TYPE                                                  3
                    vv
clus                 STOMACH INTESTINAL ADENOCARCINOMA - TUBULAR TYPE
  21Q LOSS CNV                                                      2
  21Q LOSS WILD-TYPE                                                8
                    vv
clus                 STOMACH INTESTINAL ADENOCARCINOMA - TYPE NOT OTHERWISE SPECIFIED (NOS)
  21Q LOSS CNV                                                                            7
  21Q LOSS WILD-TYPE                                                                     21
D72V4, multiclass
                    vv
clus                 T1 T2 T3 T4
  21Q LOSS CNV        0  9 12  3
  21Q LOSS WILD-TYPE  6 43 44 15
D72V5, multiclass
    clus
vv   21Q LOSS CNV 21Q LOSS WILD-TYPE
  T1            0                  6
  T2            9                 43
  T3           12                 44
  T4            3                 15
                    vv
clus                 N0 N1 N2 N3
  21Q LOSS CNV        8  9  4  4
  21Q LOSS WILD-TYPE 36 40 19 11
D72V6, multiclass
    clus
vv   21Q LOSS CNV 21Q LOSS WILD-TYPE
  N0            8                 36
  N1            9                 40
  N2            4                 19
  N3            4                 11
                    vv
clus                 M0 M1 MX
  21Q LOSS CNV       22  4  2
  21Q LOSS WILD-TYPE 96 12  6
D72V7, multiclass
    clus
vv   21Q LOSS CNV 21Q LOSS WILD-TYPE
  M0           22                 96
  M1            4                 12
  MX            2                  6
                    vv
clus                  I II III IV
  21Q LOSS CNV        5  5   7  6
  21Q LOSS WILD-TYPE 19 32  32 20
D72V8, multiclass
     clus
vv    21Q LOSS CNV 21Q LOSS WILD-TYPE
  I              5                 19
  II             5                 32
  III            7                 32
  IV             6                 20
D72V9, binary
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  21Q LOSS CNV          1   34
  21Q LOSS WILD-TYPE    4  141
     clus
vv    21Q LOSS CNV 21Q LOSS WILD-TYPE
  NO             1                  4
  YES           34                141
                    vv
clus                  R0  R1  R2  RX
  21Q LOSS CNV        23   3   3   6
  21Q LOSS WILD-TYPE 102   4   9  19
D72V10, multiclass
    clus
vv   21Q LOSS CNV 21Q LOSS WILD-TYPE
  R0           23                102
  R1            3                  4
  R2            3                  9
  RX            6                 19
D72V11, continuous

Clustering(73) Variable = 22q loss
D73V1, survival
                    sevent
clus2                  0   1
  22Q LOSS CNV        14   5
  22Q LOSS WILD-TYPE 110  14
      22Q LOSS CNV 22Q LOSS WILD-TYPE 
                19                124 
      22Q LOSS CNV 22Q LOSS WILD-TYPE 
                 5                 14 
$`22Q LOSS CNV`
TCGA-BR-6458 TCGA-BR-7715 TCGA-BR-8060 TCGA-BR-A4J1 TCGA-BR-A4QI TCGA-CD-5800 
        1.35         1.05         1.32         0.72         0.49         0.36 
TCGA-CD-5802 TCGA-CG-4438 TCGA-CG-4460 TCGA-CG-4466 TCGA-CG-5724 TCGA-CG-5725 
        0.30        54.05        21.99        18.94        12.03        15.02 
TCGA-CG-5732 TCGA-D7-5578 TCGA-D7-6519 TCGA-D7-6817 TCGA-D7-6820 TCGA-EQ-5647 
       55.04         3.58        15.65         4.70         2.93         0.62 
TCGA-FP-8631 
        0.56 

$`22Q LOSS WILD-TYPE`
TCGA-B7-5816 TCGA-B7-5818 TCGA-BR-6452 TCGA-BR-6455 TCGA-BR-6457 TCGA-BR-6563 
        5.62         0.10         0.95         1.41         1.35         0.85 
TCGA-BR-6564 TCGA-BR-6565 TCGA-BR-6566 TCGA-BR-6705 TCGA-BR-6706 TCGA-BR-6707 
        0.82         0.62         0.62         1.71         2.17         0.99 
TCGA-BR-6709 TCGA-BR-6710 TCGA-BR-6801 TCGA-BR-6802 TCGA-BR-6803 TCGA-BR-6852 
        1.22         0.66         1.12         0.76         0.66         0.26 
TCGA-BR-7196 TCGA-BR-7197 TCGA-BR-7703 TCGA-BR-7704 TCGA-BR-7707 TCGA-BR-7716 
        1.22         1.48         0.46         1.25         0.13         0.82 
TCGA-BR-7717 TCGA-BR-7722 TCGA-BR-7723 TCGA-BR-7851 TCGA-BR-7901 TCGA-BR-7957 
        0.69         0.16         4.54         0.99         0.95         0.69 
TCGA-BR-7958 TCGA-BR-7959 TCGA-BR-8059 TCGA-BR-8077 TCGA-BR-8078 TCGA-BR-8080 
        0.16         1.08         0.82         0.69         0.95         0.49 
TCGA-BR-8081 TCGA-BR-8284 TCGA-BR-8285 TCGA-BR-8286 TCGA-BR-8289 TCGA-BR-8291 
        0.46         0.72         0.26         0.43         0.26         1.18 
TCGA-BR-8295 TCGA-BR-8296 TCGA-BR-8297 TCGA-BR-8592 TCGA-BR-A4IU TCGA-BR-A4IV 
        1.55         1.48         0.76         0.20         0.59         0.92 
TCGA-BR-A4IY TCGA-BR-A4IZ TCGA-BR-A4J2 TCGA-BR-A4J4 TCGA-BR-A4J5 TCGA-BR-A4J6 
        0.39         0.79         0.79         0.53         0.43         0.13 
TCGA-BR-A4J8 TCGA-BR-A4J9 TCGA-BR-A4PF TCGA-BR-A4QL TCGA-CD-5798 TCGA-CD-5799 
        0.23         0.10         0.72         2.24         0.82         0.69 
TCGA-CD-5801 TCGA-CD-5803 TCGA-CG-4300 TCGA-CG-4301 TCGA-CG-4304 TCGA-CG-4305 
        0.49         0.07        20.02         3.02        27.02        15.95 
TCGA-CG-4306 TCGA-CG-4436 TCGA-CG-4437 TCGA-CG-4440 TCGA-CG-4441 TCGA-CG-4443 
        1.02        52.96         8.05         4.01        14.01        29.98 
TCGA-CG-4444 TCGA-CG-4449 TCGA-CG-4455 TCGA-CG-4462 TCGA-CG-4465 TCGA-CG-4469 
       47.05        19.07        12.03         1.02         8.98         7.07 
TCGA-CG-4472 TCGA-CG-4474 TCGA-CG-4477 TCGA-CG-5716 TCGA-CG-5717 TCGA-CG-5718 
       12.00         1.02         1.02         1.02         6.94         1.02 
TCGA-CG-5719 TCGA-CG-5720 TCGA-CG-5721 TCGA-CG-5722 TCGA-CG-5723 TCGA-CG-5726 
        1.02         0.99         5.98         0.95        70.06        28.96 
TCGA-CG-5727 TCGA-CG-5728 TCGA-CG-5730 TCGA-CG-5733 TCGA-CG-5734 TCGA-D7-5577 
       31.04        65.10         4.01        21.07         7.99         8.65 
TCGA-D7-5579 TCGA-D7-6518 TCGA-D7-6520 TCGA-D7-6521 TCGA-D7-6522 TCGA-D7-6524 
        4.54         9.80         9.63         8.19         6.90         0.69 
TCGA-D7-6525 TCGA-D7-6526 TCGA-D7-6527 TCGA-D7-6528 TCGA-D7-6815 TCGA-D7-6818 
        5.95         6.61         4.14         1.68         3.65         4.04 
TCGA-D7-6822 TCGA-EQ-8122 TCGA-F1-6177 TCGA-F1-6874 TCGA-F1-6875 TCGA-FP-7735 
        4.27         7.79         6.54         2.01        72.23         0.39 
TCGA-FP-7829 TCGA-FP-7916 TCGA-FP-7998 TCGA-FP-8099 TCGA-FP-8209 TCGA-FP-8210 
        0.20         3.02         3.58         1.02        59.05         5.03 
TCGA-HJ-7597 TCGA-IN-7806 TCGA-IN-7808 TCGA-IP-7968 
       26.43         6.87         3.55         2.53 

      22Q LOSS CNV 22Q LOSS WILD-TYPE 
              0.30               0.07 
      22Q LOSS CNV 22Q LOSS WILD-TYPE 
             55.04              72.23 
      22Q LOSS CNV 22Q LOSS WILD-TYPE 
              2.93               1.20 
[1] "0.3 - 55.0 (2.9)" "0.1 - 72.2 (1.2)"
        TCGA-B7-5816         TCGA-B7-5818         TCGA-BR-6452 
"22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" 
        TCGA-BR-6455         TCGA-BR-6457         TCGA-BR-6458 
"22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE"       "22Q LOSS CNV" 
        TCGA-BR-6563         TCGA-BR-6564         TCGA-BR-6565 
"22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" 
        TCGA-BR-6566         TCGA-BR-6705         TCGA-BR-6706 
"22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" 
        TCGA-BR-6707         TCGA-BR-6709         TCGA-BR-6710 
"22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" 
        TCGA-BR-6801         TCGA-BR-6802         TCGA-BR-6803 
"22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" 
        TCGA-BR-6852         TCGA-BR-7196         TCGA-BR-7197 
"22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" 
        TCGA-BR-7703         TCGA-BR-7704         TCGA-BR-7707 
"22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" 
        TCGA-BR-7715         TCGA-BR-7716         TCGA-BR-7717 
      "22Q LOSS CNV" "22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" 
        TCGA-BR-7722         TCGA-BR-7723         TCGA-BR-7851 
"22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" 
        TCGA-BR-7901         TCGA-BR-7957         TCGA-BR-7958 
"22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" 
        TCGA-BR-7959         TCGA-BR-8059         TCGA-BR-8060 
"22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE"       "22Q LOSS CNV" 
        TCGA-BR-8077         TCGA-BR-8078         TCGA-BR-8080 
"22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" 
        TCGA-BR-8081         TCGA-BR-8284         TCGA-BR-8285 
"22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" 
        TCGA-BR-8286         TCGA-BR-8289         TCGA-BR-8291 
"22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" 
        TCGA-BR-8295         TCGA-BR-8296         TCGA-BR-8297 
"22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" 
        TCGA-BR-8592         TCGA-BR-A4IU         TCGA-BR-A4IV 
"22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" 
        TCGA-BR-A4IY         TCGA-BR-A4IZ         TCGA-BR-A4J1 
"22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE"       "22Q LOSS CNV" 
        TCGA-BR-A4J2         TCGA-BR-A4J4         TCGA-BR-A4J5 
"22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" 
        TCGA-BR-A4J6         TCGA-BR-A4J8         TCGA-BR-A4J9 
"22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" 
        TCGA-BR-A4PF         TCGA-BR-A4QI         TCGA-BR-A4QL 
"22Q LOSS WILD-TYPE"       "22Q LOSS CNV" "22Q LOSS WILD-TYPE" 
        TCGA-CD-5798         TCGA-CD-5799         TCGA-CD-5800 
"22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE"       "22Q LOSS CNV" 
        TCGA-CD-5801         TCGA-CD-5802         TCGA-CD-5803 
"22Q LOSS WILD-TYPE"       "22Q LOSS CNV" "22Q LOSS WILD-TYPE" 
        TCGA-CG-4300         TCGA-CG-4301         TCGA-CG-4304 
"22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" 
        TCGA-CG-4305         TCGA-CG-4306         TCGA-CG-4436 
"22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" 
        TCGA-CG-4437         TCGA-CG-4438         TCGA-CG-4440 
"22Q LOSS WILD-TYPE"       "22Q LOSS CNV" "22Q LOSS WILD-TYPE" 
        TCGA-CG-4441         TCGA-CG-4443         TCGA-CG-4444 
"22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" 
        TCGA-CG-4449         TCGA-CG-4455         TCGA-CG-4460 
"22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE"       "22Q LOSS CNV" 
        TCGA-CG-4462         TCGA-CG-4465         TCGA-CG-4466 
"22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE"       "22Q LOSS CNV" 
        TCGA-CG-4469         TCGA-CG-4472         TCGA-CG-4474 
"22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" 
        TCGA-CG-4477         TCGA-CG-5716         TCGA-CG-5717 
"22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" 
        TCGA-CG-5718         TCGA-CG-5719         TCGA-CG-5720 
"22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" 
        TCGA-CG-5721         TCGA-CG-5722         TCGA-CG-5723 
"22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" 
        TCGA-CG-5724         TCGA-CG-5725         TCGA-CG-5726 
      "22Q LOSS CNV"       "22Q LOSS CNV" "22Q LOSS WILD-TYPE" 
        TCGA-CG-5727         TCGA-CG-5728         TCGA-CG-5730 
"22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" 
        TCGA-CG-5732         TCGA-CG-5733         TCGA-CG-5734 
      "22Q LOSS CNV" "22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" 
        TCGA-D7-5577         TCGA-D7-5578         TCGA-D7-5579 
"22Q LOSS WILD-TYPE"       "22Q LOSS CNV" "22Q LOSS WILD-TYPE" 
        TCGA-D7-6518         TCGA-D7-6519         TCGA-D7-6520 
"22Q LOSS WILD-TYPE"       "22Q LOSS CNV" "22Q LOSS WILD-TYPE" 
        TCGA-D7-6521         TCGA-D7-6522         TCGA-D7-6524 
"22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" 
        TCGA-D7-6525         TCGA-D7-6526         TCGA-D7-6527 
"22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" 
        TCGA-D7-6528         TCGA-D7-6815         TCGA-D7-6817 
"22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE"       "22Q LOSS CNV" 
        TCGA-D7-6818         TCGA-D7-6820         TCGA-D7-6822 
"22Q LOSS WILD-TYPE"       "22Q LOSS CNV" "22Q LOSS WILD-TYPE" 
        TCGA-EQ-5647         TCGA-EQ-8122         TCGA-F1-6177 
      "22Q LOSS CNV" "22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" 
        TCGA-F1-6874         TCGA-F1-6875         TCGA-FP-7735 
"22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" 
        TCGA-FP-7829         TCGA-FP-7916         TCGA-FP-7998 
"22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" 
        TCGA-FP-8099         TCGA-FP-8209         TCGA-FP-8210 
"22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" 
        TCGA-FP-8631         TCGA-HJ-7597         TCGA-IN-7806 
      "22Q LOSS CNV" "22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" 
        TCGA-IN-7808         TCGA-IP-7968 
"22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" 
        TCGA-B7-5816         TCGA-B7-5818         TCGA-BR-6452 
"22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" 
        TCGA-BR-6455         TCGA-BR-6457         TCGA-BR-6458 
"22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE"       "22Q LOSS CNV" 
        TCGA-BR-6563         TCGA-BR-6564         TCGA-BR-6565 
"22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" 
        TCGA-BR-6566         TCGA-BR-6705         TCGA-BR-6706 
"22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" 
        TCGA-BR-6707         TCGA-BR-6709         TCGA-BR-6710 
"22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" 
        TCGA-BR-6801         TCGA-BR-6802         TCGA-BR-6803 
"22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" 
        TCGA-BR-6852         TCGA-BR-7196         TCGA-BR-7197 
"22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" 
        TCGA-BR-7703         TCGA-BR-7704         TCGA-BR-7707 
"22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" 
        TCGA-BR-7715         TCGA-BR-7716         TCGA-BR-7717 
      "22Q LOSS CNV" "22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" 
        TCGA-BR-7722         TCGA-BR-7723         TCGA-BR-7851 
"22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" 
        TCGA-BR-7901         TCGA-BR-7957         TCGA-BR-7958 
"22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" 
        TCGA-BR-7959         TCGA-BR-8059         TCGA-BR-8060 
"22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE"       "22Q LOSS CNV" 
        TCGA-BR-8077         TCGA-BR-8078         TCGA-BR-8080 
"22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" 
        TCGA-BR-8081         TCGA-BR-8284         TCGA-BR-8285 
"22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" 
        TCGA-BR-8286         TCGA-BR-8289         TCGA-BR-8291 
"22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" 
        TCGA-BR-8295         TCGA-BR-8296         TCGA-BR-8297 
"22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" 
        TCGA-BR-8592         TCGA-BR-A4IU         TCGA-BR-A4IV 
"22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" 
        TCGA-BR-A4IY         TCGA-BR-A4IZ         TCGA-BR-A4J1 
"22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE"       "22Q LOSS CNV" 
        TCGA-BR-A4J2         TCGA-BR-A4J4         TCGA-BR-A4J5 
"22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" 
        TCGA-BR-A4J6         TCGA-BR-A4J8         TCGA-BR-A4J9 
"22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" 
        TCGA-BR-A4PF         TCGA-BR-A4QI         TCGA-BR-A4QL 
"22Q LOSS WILD-TYPE"       "22Q LOSS CNV" "22Q LOSS WILD-TYPE" 
        TCGA-CD-5798         TCGA-CD-5799         TCGA-CD-5800 
"22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE"       "22Q LOSS CNV" 
        TCGA-CD-5801         TCGA-CD-5802         TCGA-CD-5803 
"22Q LOSS WILD-TYPE"       "22Q LOSS CNV" "22Q LOSS WILD-TYPE" 
        TCGA-CG-4300         TCGA-CG-4301         TCGA-CG-4304 
"22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" 
        TCGA-CG-4305         TCGA-CG-4306         TCGA-CG-4436 
"22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" 
        TCGA-CG-4437         TCGA-CG-4438         TCGA-CG-4440 
"22Q LOSS WILD-TYPE"       "22Q LOSS CNV" "22Q LOSS WILD-TYPE" 
        TCGA-CG-4441         TCGA-CG-4443         TCGA-CG-4444 
"22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" 
        TCGA-CG-4449         TCGA-CG-4455         TCGA-CG-4460 
"22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE"       "22Q LOSS CNV" 
        TCGA-CG-4462         TCGA-CG-4465         TCGA-CG-4466 
"22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE"       "22Q LOSS CNV" 
        TCGA-CG-4469         TCGA-CG-4472         TCGA-CG-4474 
"22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" 
        TCGA-CG-4477         TCGA-CG-5716         TCGA-CG-5717 
"22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" 
        TCGA-CG-5718         TCGA-CG-5719         TCGA-CG-5720 
"22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" 
        TCGA-CG-5721         TCGA-CG-5722         TCGA-CG-5723 
"22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" 
        TCGA-CG-5724         TCGA-CG-5725         TCGA-CG-5726 
      "22Q LOSS CNV"       "22Q LOSS CNV" "22Q LOSS WILD-TYPE" 
        TCGA-CG-5727         TCGA-CG-5728         TCGA-CG-5730 
"22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" 
        TCGA-CG-5732         TCGA-CG-5733         TCGA-CG-5734 
      "22Q LOSS CNV" "22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" 
        TCGA-D7-5577         TCGA-D7-5578         TCGA-D7-5579 
"22Q LOSS WILD-TYPE"       "22Q LOSS CNV" "22Q LOSS WILD-TYPE" 
        TCGA-D7-6518         TCGA-D7-6519         TCGA-D7-6520 
"22Q LOSS WILD-TYPE"       "22Q LOSS CNV" "22Q LOSS WILD-TYPE" 
        TCGA-D7-6521         TCGA-D7-6522         TCGA-D7-6524 
"22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" 
        TCGA-D7-6525         TCGA-D7-6526         TCGA-D7-6527 
"22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" 
        TCGA-D7-6528         TCGA-D7-6815         TCGA-D7-6817 
"22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE"       "22Q LOSS CNV" 
        TCGA-D7-6818         TCGA-D7-6820         TCGA-D7-6822 
"22Q LOSS WILD-TYPE"       "22Q LOSS CNV" "22Q LOSS WILD-TYPE" 
        TCGA-EQ-5647         TCGA-EQ-8122         TCGA-F1-6177 
      "22Q LOSS CNV" "22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" 
        TCGA-F1-6874         TCGA-F1-6875         TCGA-FP-7735 
"22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" 
        TCGA-FP-7829         TCGA-FP-7916         TCGA-FP-7998 
"22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" 
        TCGA-FP-8099         TCGA-FP-8209         TCGA-FP-8210 
"22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" 
        TCGA-FP-8631         TCGA-HJ-7597         TCGA-IN-7806 
      "22Q LOSS CNV" "22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" 
        TCGA-IN-7808         TCGA-IP-7968 
"22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" 
        TCGA-B7-5816         TCGA-B7-5818         TCGA-BR-6452 
"22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" 
        TCGA-BR-6455         TCGA-BR-6457         TCGA-BR-6458 
"22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE"       "22Q LOSS CNV" 
        TCGA-BR-6563         TCGA-BR-6564         TCGA-BR-6565 
"22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" 
        TCGA-BR-6566         TCGA-BR-6705         TCGA-BR-6706 
"22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" 
        TCGA-BR-6707         TCGA-BR-6709         TCGA-BR-6710 
"22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" 
        TCGA-BR-6801         TCGA-BR-6802         TCGA-BR-6803 
"22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" 
        TCGA-BR-6852         TCGA-BR-7196         TCGA-BR-7197 
"22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" 
        TCGA-BR-7703         TCGA-BR-7704         TCGA-BR-7707 
"22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" 
        TCGA-BR-7715         TCGA-BR-7716         TCGA-BR-7717 
      "22Q LOSS CNV" "22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" 
        TCGA-BR-7722         TCGA-BR-7723         TCGA-BR-7851 
"22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" 
        TCGA-BR-7901         TCGA-BR-7957         TCGA-BR-7958 
"22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" 
        TCGA-BR-7959         TCGA-BR-8059         TCGA-BR-8060 
"22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE"       "22Q LOSS CNV" 
        TCGA-BR-8077         TCGA-BR-8078         TCGA-BR-8080 
"22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" 
        TCGA-BR-8081         TCGA-BR-8284         TCGA-BR-8285 
"22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" 
        TCGA-BR-8286         TCGA-BR-8289         TCGA-BR-8291 
"22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" 
        TCGA-BR-8295         TCGA-BR-8296         TCGA-BR-8297 
"22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" 
        TCGA-BR-8592         TCGA-BR-A4IU         TCGA-BR-A4IV 
"22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" 
        TCGA-BR-A4IY         TCGA-BR-A4IZ         TCGA-BR-A4J1 
"22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE"       "22Q LOSS CNV" 
        TCGA-BR-A4J2         TCGA-BR-A4J4         TCGA-BR-A4J5 
"22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" 
        TCGA-BR-A4J6         TCGA-BR-A4J8         TCGA-BR-A4J9 
"22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" 
        TCGA-BR-A4PF         TCGA-BR-A4QI         TCGA-BR-A4QL 
"22Q LOSS WILD-TYPE"       "22Q LOSS CNV" "22Q LOSS WILD-TYPE" 
        TCGA-CD-5798         TCGA-CD-5799         TCGA-CD-5800 
"22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE"       "22Q LOSS CNV" 
        TCGA-CD-5801         TCGA-CD-5802         TCGA-CD-5803 
"22Q LOSS WILD-TYPE"       "22Q LOSS CNV" "22Q LOSS WILD-TYPE" 
        TCGA-CG-4300         TCGA-CG-4301         TCGA-CG-4304 
"22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" 
        TCGA-CG-4305         TCGA-CG-4306         TCGA-CG-4436 
"22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" 
        TCGA-CG-4437         TCGA-CG-4438         TCGA-CG-4440 
"22Q LOSS WILD-TYPE"       "22Q LOSS CNV" "22Q LOSS WILD-TYPE" 
        TCGA-CG-4441         TCGA-CG-4443         TCGA-CG-4444 
"22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" 
        TCGA-CG-4449         TCGA-CG-4455         TCGA-CG-4460 
"22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE"       "22Q LOSS CNV" 
        TCGA-CG-4462         TCGA-CG-4465         TCGA-CG-4466 
"22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE"       "22Q LOSS CNV" 
        TCGA-CG-4469         TCGA-CG-4472         TCGA-CG-4474 
"22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" 
        TCGA-CG-4477         TCGA-CG-5716         TCGA-CG-5717 
"22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" 
        TCGA-CG-5718         TCGA-CG-5719         TCGA-CG-5720 
"22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" 
        TCGA-CG-5721         TCGA-CG-5722         TCGA-CG-5723 
"22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" 
        TCGA-CG-5724         TCGA-CG-5725         TCGA-CG-5726 
      "22Q LOSS CNV"       "22Q LOSS CNV" "22Q LOSS WILD-TYPE" 
        TCGA-CG-5727         TCGA-CG-5728         TCGA-CG-5730 
"22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" 
        TCGA-CG-5732         TCGA-CG-5733         TCGA-CG-5734 
      "22Q LOSS CNV" "22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" 
        TCGA-D7-5577         TCGA-D7-5578         TCGA-D7-5579 
"22Q LOSS WILD-TYPE"       "22Q LOSS CNV" "22Q LOSS WILD-TYPE" 
        TCGA-D7-6518         TCGA-D7-6519         TCGA-D7-6520 
"22Q LOSS WILD-TYPE"       "22Q LOSS CNV" "22Q LOSS WILD-TYPE" 
        TCGA-D7-6521         TCGA-D7-6522         TCGA-D7-6524 
"22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" 
        TCGA-D7-6525         TCGA-D7-6526         TCGA-D7-6527 
"22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" 
        TCGA-D7-6528         TCGA-D7-6815         TCGA-D7-6817 
"22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE"       "22Q LOSS CNV" 
        TCGA-D7-6818         TCGA-D7-6820         TCGA-D7-6822 
"22Q LOSS WILD-TYPE"       "22Q LOSS CNV" "22Q LOSS WILD-TYPE" 
        TCGA-EQ-5647         TCGA-EQ-8122         TCGA-F1-6177 
      "22Q LOSS CNV" "22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" 
        TCGA-F1-6874         TCGA-F1-6875         TCGA-FP-7735 
"22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" 
        TCGA-FP-7829         TCGA-FP-7916         TCGA-FP-7998 
"22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" 
        TCGA-FP-8099         TCGA-FP-8209         TCGA-FP-8210 
"22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" 
        TCGA-FP-8631         TCGA-HJ-7597         TCGA-IN-7806 
      "22Q LOSS CNV" "22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" 
        TCGA-IN-7808         TCGA-IP-7968 
"22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" 
[1] "hr=" "1.7"
D73V2, continuous
D73V3, binary
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  22Q LOSS CNV         10   15
  22Q LOSS WILD-TYPE   62   93
        clus
vv       22Q LOSS CNV 22Q LOSS WILD-TYPE
  FEMALE           10                 62
  MALE             15                 93
                    vv
clus                 STOMACH  ADENOCARCINOMA  DIFFUSE TYPE
  22Q LOSS CNV                                           0
  22Q LOSS WILD-TYPE                                    10
                    vv
clus                 STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  22Q LOSS CNV                                                            3
  22Q LOSS WILD-TYPE                                                     13
                    vv
clus                 STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  22Q LOSS CNV                                                                       1
  22Q LOSS WILD-TYPE                                                                 7
                    vv
clus                 STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE
  22Q LOSS CNV                                                              0
  22Q LOSS WILD-TYPE                                                        3
                    vv
clus                 STOMACH ADENOCARCINOMA  SIGNET RING TYPE
  22Q LOSS CNV                                              0
  22Q LOSS WILD-TYPE                                        1
                    vv
clus                 STOMACH ADENOCARCINOMA - DIFFUSE TYPE
  22Q LOSS CNV                                           2
  22Q LOSS WILD-TYPE                                    14
                    vv
clus                 STOMACH ADENOCARCINOMA - NOT OTHERWISE SPECIFIED (NOS)
  22Q LOSS CNV                                                           10
  22Q LOSS WILD-TYPE                                                     63
                    vv
clus                 STOMACH INTESTINAL ADENOCARCINOMA - MUCINOUS TYPE
  22Q LOSS CNV                                                       0
  22Q LOSS WILD-TYPE                                                 7
                    vv
clus                 STOMACH INTESTINAL ADENOCARCINOMA - PAPILLARY TYPE
  22Q LOSS CNV                                                        1
  22Q LOSS WILD-TYPE                                                  2
                    vv
clus                 STOMACH INTESTINAL ADENOCARCINOMA - TUBULAR TYPE
  22Q LOSS CNV                                                      4
  22Q LOSS WILD-TYPE                                                6
                    vv
clus                 STOMACH INTESTINAL ADENOCARCINOMA - TYPE NOT OTHERWISE SPECIFIED (NOS)
  22Q LOSS CNV                                                                            4
  22Q LOSS WILD-TYPE                                                                     24
D73V4, multiclass
                    vv
clus                 T1 T2 T3 T4
  22Q LOSS CNV        0  9  8  3
  22Q LOSS WILD-TYPE  6 43 48 15
D73V5, multiclass
    clus
vv   22Q LOSS CNV 22Q LOSS WILD-TYPE
  T1            0                  6
  T2            9                 43
  T3            8                 48
  T4            3                 15
                    vv
clus                 N0 N1 N2 N3
  22Q LOSS CNV        7  7  2  4
  22Q LOSS WILD-TYPE 37 42 21 11
D73V6, multiclass
    clus
vv   22Q LOSS CNV 22Q LOSS WILD-TYPE
  N0            7                 37
  N1            7                 42
  N2            2                 21
  N3            4                 11
                    vv
clus                  M0  M1  MX
  22Q LOSS CNV        17   3   1
  22Q LOSS WILD-TYPE 101  13   7
D73V7, multiclass
    clus
vv   22Q LOSS CNV 22Q LOSS WILD-TYPE
  M0           17                101
  M1            3                 13
  MX            1                  7
                    vv
clus                  I II III IV
  22Q LOSS CNV        4  6   4  5
  22Q LOSS WILD-TYPE 20 31  35 21
D73V8, multiclass
     clus
vv    22Q LOSS CNV 22Q LOSS WILD-TYPE
  I              4                 20
  II             6                 31
  III            4                 35
  IV             5                 21
D73V9, binary
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  22Q LOSS CNV          1   24
  22Q LOSS WILD-TYPE    4  151
     clus
vv    22Q LOSS CNV 22Q LOSS WILD-TYPE
  NO             1                  4
  YES           24                151
                    vv
clus                  R0  R1  R2  RX
  22Q LOSS CNV        15   1   3   4
  22Q LOSS WILD-TYPE 110   6   9  21
D73V10, multiclass
    clus
vv   22Q LOSS CNV 22Q LOSS WILD-TYPE
  R0           15                110
  R1            1                  6
  R2            3                  9
  RX            4                 21
D73V11, continuous

Clustering(74) Variable = Xq loss
D74V1, survival
                   sevent
clus2                 0   1
  XQ LOSS CNV         3   2
  XQ LOSS WILD-TYPE 121  17
      XQ LOSS CNV XQ LOSS WILD-TYPE 
                5               138 
      XQ LOSS CNV XQ LOSS WILD-TYPE 
                2                17 
$`XQ LOSS CNV`
TCGA-BR-A4PF TCGA-BR-A4QI TCGA-CG-4469 TCGA-CG-5725 TCGA-D7-6519 
        0.72         0.49         7.07        15.02        15.65 

$`XQ LOSS WILD-TYPE`
TCGA-B7-5816 TCGA-B7-5818 TCGA-BR-6452 TCGA-BR-6455 TCGA-BR-6457 TCGA-BR-6458 
        5.62         0.10         0.95         1.41         1.35         1.35 
TCGA-BR-6563 TCGA-BR-6564 TCGA-BR-6565 TCGA-BR-6566 TCGA-BR-6705 TCGA-BR-6706 
        0.85         0.82         0.62         0.62         1.71         2.17 
TCGA-BR-6707 TCGA-BR-6709 TCGA-BR-6710 TCGA-BR-6801 TCGA-BR-6802 TCGA-BR-6803 
        0.99         1.22         0.66         1.12         0.76         0.66 
TCGA-BR-6852 TCGA-BR-7196 TCGA-BR-7197 TCGA-BR-7703 TCGA-BR-7704 TCGA-BR-7707 
        0.26         1.22         1.48         0.46         1.25         0.13 
TCGA-BR-7715 TCGA-BR-7716 TCGA-BR-7717 TCGA-BR-7722 TCGA-BR-7723 TCGA-BR-7851 
        1.05         0.82         0.69         0.16         4.54         0.99 
TCGA-BR-7901 TCGA-BR-7957 TCGA-BR-7958 TCGA-BR-7959 TCGA-BR-8059 TCGA-BR-8060 
        0.95         0.69         0.16         1.08         0.82         1.32 
TCGA-BR-8077 TCGA-BR-8078 TCGA-BR-8080 TCGA-BR-8081 TCGA-BR-8284 TCGA-BR-8285 
        0.69         0.95         0.49         0.46         0.72         0.26 
TCGA-BR-8286 TCGA-BR-8289 TCGA-BR-8291 TCGA-BR-8295 TCGA-BR-8296 TCGA-BR-8297 
        0.43         0.26         1.18         1.55         1.48         0.76 
TCGA-BR-8592 TCGA-BR-A4IU TCGA-BR-A4IV TCGA-BR-A4IY TCGA-BR-A4IZ TCGA-BR-A4J1 
        0.20         0.59         0.92         0.39         0.79         0.72 
TCGA-BR-A4J2 TCGA-BR-A4J4 TCGA-BR-A4J5 TCGA-BR-A4J6 TCGA-BR-A4J8 TCGA-BR-A4J9 
        0.79         0.53         0.43         0.13         0.23         0.10 
TCGA-BR-A4QL TCGA-CD-5798 TCGA-CD-5799 TCGA-CD-5800 TCGA-CD-5801 TCGA-CD-5802 
        2.24         0.82         0.69         0.36         0.49         0.30 
TCGA-CD-5803 TCGA-CG-4300 TCGA-CG-4301 TCGA-CG-4304 TCGA-CG-4305 TCGA-CG-4306 
        0.07        20.02         3.02        27.02        15.95         1.02 
TCGA-CG-4436 TCGA-CG-4437 TCGA-CG-4438 TCGA-CG-4440 TCGA-CG-4441 TCGA-CG-4443 
       52.96         8.05        54.05         4.01        14.01        29.98 
TCGA-CG-4444 TCGA-CG-4449 TCGA-CG-4455 TCGA-CG-4460 TCGA-CG-4462 TCGA-CG-4465 
       47.05        19.07        12.03        21.99         1.02         8.98 
TCGA-CG-4466 TCGA-CG-4472 TCGA-CG-4474 TCGA-CG-4477 TCGA-CG-5716 TCGA-CG-5717 
       18.94        12.00         1.02         1.02         1.02         6.94 
TCGA-CG-5718 TCGA-CG-5719 TCGA-CG-5720 TCGA-CG-5721 TCGA-CG-5722 TCGA-CG-5723 
        1.02         1.02         0.99         5.98         0.95        70.06 
TCGA-CG-5724 TCGA-CG-5726 TCGA-CG-5727 TCGA-CG-5728 TCGA-CG-5730 TCGA-CG-5732 
       12.03        28.96        31.04        65.10         4.01        55.04 
TCGA-CG-5733 TCGA-CG-5734 TCGA-D7-5577 TCGA-D7-5578 TCGA-D7-5579 TCGA-D7-6518 
       21.07         7.99         8.65         3.58         4.54         9.80 
TCGA-D7-6520 TCGA-D7-6521 TCGA-D7-6522 TCGA-D7-6524 TCGA-D7-6525 TCGA-D7-6526 
        9.63         8.19         6.90         0.69         5.95         6.61 
TCGA-D7-6527 TCGA-D7-6528 TCGA-D7-6815 TCGA-D7-6817 TCGA-D7-6818 TCGA-D7-6820 
        4.14         1.68         3.65         4.70         4.04         2.93 
TCGA-D7-6822 TCGA-EQ-5647 TCGA-EQ-8122 TCGA-F1-6177 TCGA-F1-6874 TCGA-F1-6875 
        4.27         0.62         7.79         6.54         2.01        72.23 
TCGA-FP-7735 TCGA-FP-7829 TCGA-FP-7916 TCGA-FP-7998 TCGA-FP-8099 TCGA-FP-8209 
        0.39         0.20         3.02         3.58         1.02        59.05 
TCGA-FP-8210 TCGA-FP-8631 TCGA-HJ-7597 TCGA-IN-7806 TCGA-IN-7808 TCGA-IP-7968 
        5.03         0.56        26.43         6.87         3.55         2.53 

      XQ LOSS CNV XQ LOSS WILD-TYPE 
             0.49              0.07 
      XQ LOSS CNV XQ LOSS WILD-TYPE 
            15.65             72.23 
      XQ LOSS CNV XQ LOSS WILD-TYPE 
            7.070             1.235 
[1] "0.5 - 15.7 (7.1)" "0.1 - 72.2 (1.2)"
       TCGA-B7-5816        TCGA-B7-5818        TCGA-BR-6452        TCGA-BR-6455 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-BR-6457        TCGA-BR-6458        TCGA-BR-6563        TCGA-BR-6564 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-BR-6565        TCGA-BR-6566        TCGA-BR-6705        TCGA-BR-6706 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-BR-6707        TCGA-BR-6709        TCGA-BR-6710        TCGA-BR-6801 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-BR-6802        TCGA-BR-6803        TCGA-BR-6852        TCGA-BR-7196 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-BR-7197        TCGA-BR-7703        TCGA-BR-7704        TCGA-BR-7707 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-BR-7715        TCGA-BR-7716        TCGA-BR-7717        TCGA-BR-7722 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-BR-7723        TCGA-BR-7851        TCGA-BR-7901        TCGA-BR-7957 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-BR-7958        TCGA-BR-7959        TCGA-BR-8059        TCGA-BR-8060 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-BR-8077        TCGA-BR-8078        TCGA-BR-8080        TCGA-BR-8081 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-BR-8284        TCGA-BR-8285        TCGA-BR-8286        TCGA-BR-8289 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-BR-8291        TCGA-BR-8295        TCGA-BR-8296        TCGA-BR-8297 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-BR-8592        TCGA-BR-A4IU        TCGA-BR-A4IV        TCGA-BR-A4IY 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-BR-A4IZ        TCGA-BR-A4J1        TCGA-BR-A4J2        TCGA-BR-A4J4 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-BR-A4J5        TCGA-BR-A4J6        TCGA-BR-A4J8        TCGA-BR-A4J9 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-BR-A4PF        TCGA-BR-A4QI        TCGA-BR-A4QL        TCGA-CD-5798 
      "XQ LOSS CNV"       "XQ LOSS CNV" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-CD-5799        TCGA-CD-5800        TCGA-CD-5801        TCGA-CD-5802 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-CD-5803        TCGA-CG-4300        TCGA-CG-4301        TCGA-CG-4304 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-CG-4305        TCGA-CG-4306        TCGA-CG-4436        TCGA-CG-4437 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-CG-4438        TCGA-CG-4440        TCGA-CG-4441        TCGA-CG-4443 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-CG-4444        TCGA-CG-4449        TCGA-CG-4455        TCGA-CG-4460 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-CG-4462        TCGA-CG-4465        TCGA-CG-4466        TCGA-CG-4469 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE"       "XQ LOSS CNV" 
       TCGA-CG-4472        TCGA-CG-4474        TCGA-CG-4477        TCGA-CG-5716 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-CG-5717        TCGA-CG-5718        TCGA-CG-5719        TCGA-CG-5720 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-CG-5721        TCGA-CG-5722        TCGA-CG-5723        TCGA-CG-5724 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-CG-5725        TCGA-CG-5726        TCGA-CG-5727        TCGA-CG-5728 
      "XQ LOSS CNV" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-CG-5730        TCGA-CG-5732        TCGA-CG-5733        TCGA-CG-5734 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-D7-5577        TCGA-D7-5578        TCGA-D7-5579        TCGA-D7-6518 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-D7-6519        TCGA-D7-6520        TCGA-D7-6521        TCGA-D7-6522 
      "XQ LOSS CNV" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-D7-6524        TCGA-D7-6525        TCGA-D7-6526        TCGA-D7-6527 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-D7-6528        TCGA-D7-6815        TCGA-D7-6817        TCGA-D7-6818 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-D7-6820        TCGA-D7-6822        TCGA-EQ-5647        TCGA-EQ-8122 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-F1-6177        TCGA-F1-6874        TCGA-F1-6875        TCGA-FP-7735 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-FP-7829        TCGA-FP-7916        TCGA-FP-7998        TCGA-FP-8099 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-FP-8209        TCGA-FP-8210        TCGA-FP-8631        TCGA-HJ-7597 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-IN-7806        TCGA-IN-7808        TCGA-IP-7968 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-B7-5816        TCGA-B7-5818        TCGA-BR-6452        TCGA-BR-6455 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-BR-6457        TCGA-BR-6458        TCGA-BR-6563        TCGA-BR-6564 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-BR-6565        TCGA-BR-6566        TCGA-BR-6705        TCGA-BR-6706 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-BR-6707        TCGA-BR-6709        TCGA-BR-6710        TCGA-BR-6801 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-BR-6802        TCGA-BR-6803        TCGA-BR-6852        TCGA-BR-7196 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-BR-7197        TCGA-BR-7703        TCGA-BR-7704        TCGA-BR-7707 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-BR-7715        TCGA-BR-7716        TCGA-BR-7717        TCGA-BR-7722 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-BR-7723        TCGA-BR-7851        TCGA-BR-7901        TCGA-BR-7957 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-BR-7958        TCGA-BR-7959        TCGA-BR-8059        TCGA-BR-8060 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-BR-8077        TCGA-BR-8078        TCGA-BR-8080        TCGA-BR-8081 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-BR-8284        TCGA-BR-8285        TCGA-BR-8286        TCGA-BR-8289 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-BR-8291        TCGA-BR-8295        TCGA-BR-8296        TCGA-BR-8297 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-BR-8592        TCGA-BR-A4IU        TCGA-BR-A4IV        TCGA-BR-A4IY 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-BR-A4IZ        TCGA-BR-A4J1        TCGA-BR-A4J2        TCGA-BR-A4J4 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-BR-A4J5        TCGA-BR-A4J6        TCGA-BR-A4J8        TCGA-BR-A4J9 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-BR-A4PF        TCGA-BR-A4QI        TCGA-BR-A4QL        TCGA-CD-5798 
      "XQ LOSS CNV"       "XQ LOSS CNV" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-CD-5799        TCGA-CD-5800        TCGA-CD-5801        TCGA-CD-5802 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-CD-5803        TCGA-CG-4300        TCGA-CG-4301        TCGA-CG-4304 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-CG-4305        TCGA-CG-4306        TCGA-CG-4436        TCGA-CG-4437 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-CG-4438        TCGA-CG-4440        TCGA-CG-4441        TCGA-CG-4443 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-CG-4444        TCGA-CG-4449        TCGA-CG-4455        TCGA-CG-4460 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-CG-4462        TCGA-CG-4465        TCGA-CG-4466        TCGA-CG-4469 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE"       "XQ LOSS CNV" 
       TCGA-CG-4472        TCGA-CG-4474        TCGA-CG-4477        TCGA-CG-5716 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-CG-5717        TCGA-CG-5718        TCGA-CG-5719        TCGA-CG-5720 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-CG-5721        TCGA-CG-5722        TCGA-CG-5723        TCGA-CG-5724 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-CG-5725        TCGA-CG-5726        TCGA-CG-5727        TCGA-CG-5728 
      "XQ LOSS CNV" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-CG-5730        TCGA-CG-5732        TCGA-CG-5733        TCGA-CG-5734 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-D7-5577        TCGA-D7-5578        TCGA-D7-5579        TCGA-D7-6518 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-D7-6519        TCGA-D7-6520        TCGA-D7-6521        TCGA-D7-6522 
      "XQ LOSS CNV" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-D7-6524        TCGA-D7-6525        TCGA-D7-6526        TCGA-D7-6527 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-D7-6528        TCGA-D7-6815        TCGA-D7-6817        TCGA-D7-6818 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-D7-6820        TCGA-D7-6822        TCGA-EQ-5647        TCGA-EQ-8122 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-F1-6177        TCGA-F1-6874        TCGA-F1-6875        TCGA-FP-7735 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-FP-7829        TCGA-FP-7916        TCGA-FP-7998        TCGA-FP-8099 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-FP-8209        TCGA-FP-8210        TCGA-FP-8631        TCGA-HJ-7597 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-IN-7806        TCGA-IN-7808        TCGA-IP-7968 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-B7-5816        TCGA-B7-5818        TCGA-BR-6452        TCGA-BR-6455 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-BR-6457        TCGA-BR-6458        TCGA-BR-6563        TCGA-BR-6564 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-BR-6565        TCGA-BR-6566        TCGA-BR-6705        TCGA-BR-6706 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-BR-6707        TCGA-BR-6709        TCGA-BR-6710        TCGA-BR-6801 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-BR-6802        TCGA-BR-6803        TCGA-BR-6852        TCGA-BR-7196 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-BR-7197        TCGA-BR-7703        TCGA-BR-7704        TCGA-BR-7707 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-BR-7715        TCGA-BR-7716        TCGA-BR-7717        TCGA-BR-7722 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-BR-7723        TCGA-BR-7851        TCGA-BR-7901        TCGA-BR-7957 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-BR-7958        TCGA-BR-7959        TCGA-BR-8059        TCGA-BR-8060 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-BR-8077        TCGA-BR-8078        TCGA-BR-8080        TCGA-BR-8081 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-BR-8284        TCGA-BR-8285        TCGA-BR-8286        TCGA-BR-8289 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-BR-8291        TCGA-BR-8295        TCGA-BR-8296        TCGA-BR-8297 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-BR-8592        TCGA-BR-A4IU        TCGA-BR-A4IV        TCGA-BR-A4IY 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-BR-A4IZ        TCGA-BR-A4J1        TCGA-BR-A4J2        TCGA-BR-A4J4 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-BR-A4J5        TCGA-BR-A4J6        TCGA-BR-A4J8        TCGA-BR-A4J9 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-BR-A4PF        TCGA-BR-A4QI        TCGA-BR-A4QL        TCGA-CD-5798 
      "XQ LOSS CNV"       "XQ LOSS CNV" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-CD-5799        TCGA-CD-5800        TCGA-CD-5801        TCGA-CD-5802 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-CD-5803        TCGA-CG-4300        TCGA-CG-4301        TCGA-CG-4304 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-CG-4305        TCGA-CG-4306        TCGA-CG-4436        TCGA-CG-4437 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-CG-4438        TCGA-CG-4440        TCGA-CG-4441        TCGA-CG-4443 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-CG-4444        TCGA-CG-4449        TCGA-CG-4455        TCGA-CG-4460 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-CG-4462        TCGA-CG-4465        TCGA-CG-4466        TCGA-CG-4469 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE"       "XQ LOSS CNV" 
       TCGA-CG-4472        TCGA-CG-4474        TCGA-CG-4477        TCGA-CG-5716 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-CG-5717        TCGA-CG-5718        TCGA-CG-5719        TCGA-CG-5720 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-CG-5721        TCGA-CG-5722        TCGA-CG-5723        TCGA-CG-5724 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-CG-5725        TCGA-CG-5726        TCGA-CG-5727        TCGA-CG-5728 
      "XQ LOSS CNV" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-CG-5730        TCGA-CG-5732        TCGA-CG-5733        TCGA-CG-5734 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-D7-5577        TCGA-D7-5578        TCGA-D7-5579        TCGA-D7-6518 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-D7-6519        TCGA-D7-6520        TCGA-D7-6521        TCGA-D7-6522 
      "XQ LOSS CNV" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-D7-6524        TCGA-D7-6525        TCGA-D7-6526        TCGA-D7-6527 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-D7-6528        TCGA-D7-6815        TCGA-D7-6817        TCGA-D7-6818 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-D7-6820        TCGA-D7-6822        TCGA-EQ-5647        TCGA-EQ-8122 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-F1-6177        TCGA-F1-6874        TCGA-F1-6875        TCGA-FP-7735 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-FP-7829        TCGA-FP-7916        TCGA-FP-7998        TCGA-FP-8099 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-FP-8209        TCGA-FP-8210        TCGA-FP-8631        TCGA-HJ-7597 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-IN-7806        TCGA-IN-7808        TCGA-IP-7968 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
[1] "hr=" "2.6"
D74V2, continuous
D74V3, binary
[1] "tbl2"
                   cls
clus                [,1] [,2]
  XQ LOSS CNV          3    5
  XQ LOSS WILD-TYPE   69  103
        clus
vv       XQ LOSS CNV XQ LOSS WILD-TYPE
  FEMALE           3                69
  MALE             5               103
                   vv
clus                STOMACH  ADENOCARCINOMA  DIFFUSE TYPE
  XQ LOSS CNV                                           0
  XQ LOSS WILD-TYPE                                    10
                   vv
clus                STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  XQ LOSS CNV                                                            2
  XQ LOSS WILD-TYPE                                                     14
                   vv
clus                STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  XQ LOSS CNV                                                                       0
  XQ LOSS WILD-TYPE                                                                 8
                   vv
clus                STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE
  XQ LOSS CNV                                                              0
  XQ LOSS WILD-TYPE                                                        3
                   vv
clus                STOMACH ADENOCARCINOMA  SIGNET RING TYPE
  XQ LOSS CNV                                              0
  XQ LOSS WILD-TYPE                                        1
                   vv
clus                STOMACH ADENOCARCINOMA - DIFFUSE TYPE
  XQ LOSS CNV                                           1
  XQ LOSS WILD-TYPE                                    15
                   vv
clus                STOMACH ADENOCARCINOMA - NOT OTHERWISE SPECIFIED (NOS)
  XQ LOSS CNV                                                            2
  XQ LOSS WILD-TYPE                                                     71
                   vv
clus                STOMACH INTESTINAL ADENOCARCINOMA - MUCINOUS TYPE
  XQ LOSS CNV                                                       1
  XQ LOSS WILD-TYPE                                                 6
                   vv
clus                STOMACH INTESTINAL ADENOCARCINOMA - PAPILLARY TYPE
  XQ LOSS CNV                                                        0
  XQ LOSS WILD-TYPE                                                  3
                   vv
clus                STOMACH INTESTINAL ADENOCARCINOMA - TUBULAR TYPE
  XQ LOSS CNV                                                      1
  XQ LOSS WILD-TYPE                                                9
                   vv
clus                STOMACH INTESTINAL ADENOCARCINOMA - TYPE NOT OTHERWISE SPECIFIED (NOS)
  XQ LOSS CNV                                                                            1
  XQ LOSS WILD-TYPE                                                                     27
D74V4, multiclass
                   vv
clus                T1 T2 T3 T4
  XQ LOSS CNV        0  4  1  0
  XQ LOSS WILD-TYPE  6 48 55 18
D74V5, multiclass
    clus
vv   XQ LOSS CNV XQ LOSS WILD-TYPE
  T1           0                 6
  T2           4                48
  T3           1                55
  T4           0                18
                   vv
clus                N0 N1 N2 N3
  XQ LOSS CNV        1  2  0  2
  XQ LOSS WILD-TYPE 43 47 23 13
D74V6, multiclass
    clus
vv   XQ LOSS CNV XQ LOSS WILD-TYPE
  N0           1                43
  N1           2                47
  N2           0                23
  N3           2                13
                   vv
clus                 M0  M1  MX
  XQ LOSS CNV         6   0   0
  XQ LOSS WILD-TYPE 112  16   8
D74V7, multiclass
    clus
vv   XQ LOSS CNV XQ LOSS WILD-TYPE
  M0           6               112
  M1           0                16
  MX           0                 8
                   vv
clus                 I II III IV
  XQ LOSS CNV        1  0   1  2
  XQ LOSS WILD-TYPE 23 37  38 24
D74V8, multiclass
     clus
vv    XQ LOSS CNV XQ LOSS WILD-TYPE
  I             1                23
  II            0                37
  III           1                38
  IV            2                24
D74V9, binary
[1] "tbl2"
                   cls
clus                [,1] [,2]
  XQ LOSS CNV          1    7
  XQ LOSS WILD-TYPE    4  168
     clus
vv    XQ LOSS CNV XQ LOSS WILD-TYPE
  NO            1                 4
  YES           7               168
                   vv
clus                 R0  R1  R2  RX
  XQ LOSS CNV         4   2   0   2
  XQ LOSS WILD-TYPE 121   5  12  23
D74V10, multiclass
    clus
vv   XQ LOSS CNV XQ LOSS WILD-TYPE
  R0           4               121
  R1           2                 5
  R2           0                12
  RX           2                23
D74V11, continuous
                                    V1.D 
                         "Time to Death" 
                                      V2 
                                   "AGE" 
                                      V3 
                                "GENDER" 
                                      V4 
                     "HISTOLOGICAL.TYPE" 
                                      V5 
                           "PATHOLOGY.T" 
                                      V6 
                           "PATHOLOGY.N" 
                                      V7 
                   "PATHOLOGICSPREAD(M)" 
                                      V8 
                           "TUMOR.STAGE" 
                                      V9 
"RADIATIONS.RADIATION.REGIMENINDICATION" 
                                     V10 
             "COMPLETENESS.OF.RESECTION" 
                                     V11 
                 "NUMBER.OF.LYMPH.NODES" 
> q(save="no")
